github-actions[bot]
commented
4 days ago Test Results (powered by Planemo)
Test Summary
| Test State | Count |
|---|---|
| Total | 1 |
| Passed | 1 |
| Error | 0 |
| Failure | 0 |
| Skipped | 0 |
Passed Tests
*✅ rnaseq-de-filtering-plotting.ga_0
#### Workflow invocation details
* Invocation Messages
*
Steps
- **Step 1: Counts from changed condition**: * step_state: scheduled - **Step 2: Counts from reference condition**: * step_state: scheduled - **Step 11: Differential Analysis**: * step_state: scheduled *Jobs
- **Job 1:** * Job state is ok **Command Line:** * ```console cat '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/deseq2/9a882d108833/deseq2/get_deseq_dataset.R' > /dev/null && Rscript '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/deseq2/9a882d108833/deseq2/deseq2.R' --cores ${GALAXY_SLOTS:-1} -o '/tmp/tmpz12vnfdi/job_working_directory/000/10/outputs/dataset_68c0f91c-cfa0-4c43-9a35-3d50f6e082db.dat' -p '/tmp/tmpz12vnfdi/job_working_directory/000/10/outputs/dataset_85aa60fa-bcad-46eb-87d5-a47d4cb672a3.dat' -A 0.1 -n '/tmp/tmpz12vnfdi/job_working_directory/000/10/outputs/dataset_2f8a5393-62c6-4052-816b-6ee3379a9676.dat' -H -f '[["DEFactor", [{"BaseFactor": ["/tmp/tmpz12vnfdi/files/4/3/e/dataset_43eb9297-810e-41c7-a8ca-6146e3d4e819.dat", "/tmp/tmpz12vnfdi/files/c/8/4/dataset_c849c55e-b6f5-4071-ad64-07865a53b5b4.dat"]}, {"MainFactor": ["/tmp/tmpz12vnfdi/files/e/a/2/dataset_ea2c1d5d-b714-4932-8ce7-e9711931600d.dat", "/tmp/tmpz12vnfdi/files/b/6/0/dataset_b601ca20-9f26-46fe-930c-a35dc9610462.dat"]}]]]' -l '{"dataset_ea2c1d5d-b714-4932-8ce7-e9711931600d.dat": "SRR5085169 Counts Table", "dataset_b601ca20-9f26-46fe-930c-a35dc9610462.dat": "SRR5085170 Counts Table", "dataset_43eb9297-810e-41c7-a8ca-6146e3d4e819.dat": "SRR5085167 Counts Table", "dataset_c849c55e-b6f5-4071-ad64-07865a53b5b4.dat": "SRR5085168 Counts Table"}' -t 1 ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing Warning message: `aes_string()` was deprecated in ggplot2 3.0.0. ℹ Please use tidy evaluation idioms with `aes()`. ℹ See also `vignette("ggplot2-in-packages")` for more information. ``` **Standard Output:** * ```console primary factor: DEFactor --------------------- No size factor was used DESeq2 run information sample table: DEFactor SRR5085167 Counts Table BaseFactor SRR5085168 Counts Table BaseFactor SRR5085169 Counts Table MainFactor SRR5085170 Counts Table MainFactor design formula: ~DEFactor 4 samples with counts over 7127 genes Applied default - beta prior off [1] "use_beta_prior is set to FALSE" using disperion fit type: parametric creating plots summary of results DEFactor: MainFactor vs BaseFactor out of 5734 with nonzero total read count adjusted p-value < 0.1 LFC > 0 (up) : 2, 0.035% LFC < 0 (down) : 13, 0.23% outliers [1] : 0, 0% low counts [2] : 2963, 52% (mean count < 7) [1] see 'cooksCutoff' argument of ?results [2] see 'independentFiltering' argument of ?results NULL closing plot device null device 1 Session information: R version 4.3.1 (2023-06-16) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.23.so; LAPACK version 3.11.0 locale: [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C time zone: NA tzcode source: system (glibc) attached base packages: [1] stats4 tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] pheatmap_1.0.12 ggrepel_0.9.3 [3] ggplot2_3.4.2 rjson_0.2.21 [5] gplots_3.1.3 RColorBrewer_1.1-3 [7] DESeq2_1.40.2 SummarizedExperiment_1.30.2 [9] Biobase_2.60.0 MatrixGenerics_1.12.2 [11] matrixStats_1.0.0 GenomicRanges_1.52.0 [13] GenomeInfoDb_1.36.1 IRanges_2.34.1 [15] S4Vectors_0.38.1 BiocGenerics_0.46.0 [17] getopt_1.20.3 loaded via a namespace (and not attached): [1] utf8_1.2.3 generics_0.1.3 bitops_1.0-7 [4] KernSmooth_2.23-22 gtools_3.9.4 lattice_0.21-8 [7] caTools_1.18.2 magrittr_2.0.3 grid_4.3.1 [10] Matrix_1.6-0 fansi_1.0.4 scales_1.2.1 [13] codetools_0.2-19 cli_3.6.1 rlang_1.1.1 [16] crayon_1.5.2 XVector_0.40.0 munsell_0.5.0 [19] withr_2.5.0 DelayedArray_0.26.6 S4Arrays_1.0.4 [22] parallel_4.3.1 BiocParallel_1.34.2 dplyr_1.1.2 [25] colorspace_2.1-0 locfit_1.5-9.8 GenomeInfoDbData_1.2.10 [28] vctrs_0.6.3 R6_2.5.1 lifecycle_1.0.3 [31] zlibbioc_1.46.0 pkgconfig_2.0.3 pillar_1.9.0 [34] gtable_0.3.3 glue_1.6.2 Rcpp_1.0.11 [37] tibble_3.2.1 tidyselect_1.2.0 farver_2.1.1 [40] labeling_0.4.2 compiler_4.3.1 RCurl_1.98-1.12 ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "2770ba06a57011ef9545c98e6440421e" ` | | advanced\_options | ` {"auto_mean_filter_off": false, "esf_cond": {"__current_case__": 0, "esf": ""}, "fit_type": "1", "outlier_filter_off": false, "outlier_replace_off": false, "prefilter_conditional": {"__current_case__": 1, "prefilter": ""}, "use_beta_priors": false} ` | | batch\_factors | ` None ` | | chromInfo | ` "/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | header | ` true ` | | output\_options | ` {"alpha_ma": "0.1", "output_selector": ["pdf", "normCounts"]} ` | | select\_data | ` {"__current_case__": 1, "how": "datasets_per_level", "rep_factorName": [{"__index__": 0, "factorName": "DEFactor", "rep_factorLevel": [{"__index__": 0, "countsFile": {"values": [{"id": 1, "src": "hdca"}]}, "factorLevel": "MainFactor"}, {"__index__": 1, "countsFile": {"values": [{"id": 2, "src": "hdca"}]}, "factorLevel": "BaseFactor"}]}]} ` | | tximport | ` {"__current_case__": 1, "tximport_selector": "count"} ` | - **Step 12: toolshed.g2.bx.psu.edu/repos/iuc/compose\_text\_param/compose\_text\_param/0.1.1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cd ../; python _evaluate_expression_.py
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "2770ba06a57011ef9545c98e6440421e" ` |
| chromInfo | ` "/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| components | ` [{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c7<", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 2, "component_value": "0.1", "select_param_type": "float"}}] ` |
| dbkey | ` "?" ` |
</details>
- **Step 13: toolshed.g2.bx.psu.edu/repos/iuc/compose\_text\_param/compose\_text\_param/0.1.1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cd ../; python _evaluate_expression_.py
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "2770ba06a57011ef9545c98e6440421e" ` |
| chromInfo | ` "/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| components | ` [{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "abs(c3)>", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 2, "component_value": "0.5", "select_param_type": "float"}}] ` |
| dbkey | ` "?" ` |
</details>
- **Step 14: toolshed.g2.bx.psu.edu/repos/iuc/deg\_annotate/deg\_annotate/1.1.0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/e98d4ab5b5bc/deg_annotate/deg_annotate.py' -in '/tmp/tmpz12vnfdi/files/6/8/c/dataset_68c0f91c-cfa0-4c43-9a35-3d50f6e082db.dat' -m 'degseq' -g '/tmp/tmpz12vnfdi/files/8/7/2/dataset_8727b6a8-cbb4-46a6-bd79-0dc199104131.dat' -t 'exon' -i 'gene_id' -x 'transcript_id' -a 'gene_biotype, gene_name' -o '/tmp/tmpz12vnfdi/job_working_directory/000/13/outputs/dataset_a40cfd0a-a90c-443f-bc5f-48d90f3cfec1.dat'
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
DE(X)Seq output file : /tmp/tmpz12vnfdi/files/6/8/c/dataset_68c0f91c-cfa0-4c43-9a35-3d50f6e082db.dat
Input file type : degseq
Annotation file : /tmp/tmpz12vnfdi/files/8/7/2/dataset_8727b6a8-cbb4-46a6-bd79-0dc199104131.dat
Feature type : exon
ID attribute : gene_id
Transcript attribute : transcript_id
Attributes to include : gene_biotype, gene_name
Annotated output file : /tmp/tmpz12vnfdi/job_working_directory/000/13/outputs/dataset_a40cfd0a-a90c-443f-bc5f-48d90f3cfec1.dat
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "2770ba06a57011ef9545c98e6440421e" ` |
| advanced\_parameters | ` {"gff_attributes": "gene_biotype, gene_name", "gff_feature_attribute": "gene_id", "gff_feature_type": "exon", "gff_transcript_attribute": "transcript_id"} ` |
| chromInfo | ` "/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| mode | ` "degseq" ` |
</details>
- **Step 15: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_awk\_tool/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
env -i $(which awk) --sandbox -v FS=' ' -v OFS=' ' --re-interval -f '/tmp/tmpz12vnfdi/job_working_directory/000/14/configs/tmpjoibxu0z' '/tmp/tmpz12vnfdi/files/2/f/8/dataset_2f8a5393-62c6-4052-816b-6ee3379a9676.dat' > '/tmp/tmpz12vnfdi/job_working_directory/000/14/outputs/dataset_74e4165f-1682-4435-939b-15206ca2fa46.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "2770ba06a57011ef9545c98e6440421e" ` |
| chromInfo | ` "/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "END{print NF}" ` |
| dbkey | ` "?" ` |
</details>
- **Step 16: Annotate DESeq2 table**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cat '/tmp/tmpz12vnfdi/files/9/4/3/dataset_943262f7-06a4-46a3-b2a9-ca2c09cd6642.dat' >> '/tmp/tmpz12vnfdi/job_working_directory/000/15/outputs/dataset_ea5df634-5102-43c7-895f-804d0e82d223.dat' && cat '/tmp/tmpz12vnfdi/files/a/4/0/dataset_a40cfd0a-a90c-443f-bc5f-48d90f3cfec1.dat' >> '/tmp/tmpz12vnfdi/job_working_directory/000/15/outputs/dataset_ea5df634-5102-43c7-895f-804d0e82d223.dat' && exit 0
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "2770ba06a57011ef9545c98e6440421e" ` |
| chromInfo | ` "/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| queries | ` [{"__index__": 0, "inputs2": {"values": [{"id": 15, "src": "hda"}]}}] ` |
</details>
- **Step 17: param\_value\_from\_file**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cd ../; python _evaluate_expression_.py
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "2770ba06a57011ef9545c98e6440421e" ` |
| chromInfo | ` "/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| param\_type | ` "text" ` |
| remove\_newlines | ` true ` |
</details>
- **Step 18: Filter with p-adj threshold**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
python '/tmp/tmpz12vnfdi/galaxy-dev/tools/stats/filtering.py' '/tmp/tmpz12vnfdi/files/e/a/5/dataset_ea5df634-5102-43c7-895f-804d0e82d223.dat' '/tmp/tmpz12vnfdi/job_working_directory/000/18/outputs/dataset_97245f12-45f9-477c-a596-c33ce24cbf92.dat' '/tmp/tmpz12vnfdi/job_working_directory/000/18/configs/tmpusvgoh25' 13 "str,float,float,float,float,float,float,str,int,int,str,str,str" 1
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
Filtering with c7<0.1,
kept 0.22% of 7128 valid lines (7128 total lines).
Skipped 4356 invalid line(s) starting at line #2773: "YDL246C 0.164326158122698 0.855789798651137 4.98087080202474 0.171815297498433 0.863582738705987 NA chrIV 8682 9756 - protein_coding SOR2"
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "2770ba06a57011ef9545c98e6440421e" ` |
| chromInfo | ` "/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| cond | ` "c7<0.1" ` |
| dbkey | ` "?" ` |
| header\_lines | ` "1" ` |
</details>
- **Step 19: Generate Valcanot plot of DE genes**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
Rscript '/tmp/tmpz12vnfdi/job_working_directory/000/17/configs/tmp8hjj249e'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
Removed 1393 rows containing missing values (geom_point).
```
**Standard Output:**
* ```console
null device
1
R version 4.0.5 (2021-03-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)
Matrix products: default
BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.15.so
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggrepel_0.9.1 ggplot2_3.3.3 dplyr_1.0.6
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 magrittr_2.0.1 tidyselect_1.1.1 munsell_0.5.0
[5] colorspace_2.0-1 R6_2.5.0 rlang_0.4.11 fansi_0.5.0
[9] grid_4.0.5 gtable_0.3.0 utf8_1.2.1 withr_2.4.2
[13] ellipsis_0.3.2 digest_0.6.27 tibble_3.1.2 lifecycle_1.0.0
[17] crayon_1.4.1 purrr_0.3.4 farver_2.1.0 vctrs_0.3.8
[21] glue_1.4.2 labeling_0.4.2 compiler_4.0.5 pillar_1.6.1
[25] generics_0.1.0 scales_1.1.1 pkgconfig_2.0.3
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "2770ba06a57011ef9545c98e6440421e" ` |
| chromInfo | ` "/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| fdr\_col | ` "7" ` |
| header | ` "yes" ` |
| label\_col | ` "13" ` |
| labels | ` {"__current_case__": 0, "label_select": "signif", "top_num": "10"} ` |
| lfc\_col | ` "3" ` |
| lfc\_thresh | ` "0.5" ` |
| out\_options | ` {"rscript_out": false} ` |
| plot\_options | ` {"boxes": false, "legend": null, "legend_labs": "Down,Not Sig,Up", "title": null, "xlab": null, "xmax": null, "xmin": null, "ylab": null, "ymax": null} ` |
| pval\_col | ` "6" ` |
| signif\_thresh | ` "0.1" ` |
</details>
- **Step 20: toolshed.g2.bx.psu.edu/repos/iuc/compose\_text\_param/compose\_text\_param/0.1.1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cd ../; python _evaluate_expression_.py
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "2770ba06a57011ef9545c98e6440421e" ` |
| chromInfo | ` "/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| components | ` [{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c1-c", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "5", "select_param_type": "text"}}] ` |
| dbkey | ` "?" ` |
</details>
- **Step 3: Count files have header**:
* step_state: scheduled
- **Step 21: Filter with log2 FC threshold**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
python '/tmp/tmpz12vnfdi/galaxy-dev/tools/stats/filtering.py' '/tmp/tmpz12vnfdi/files/9/7/2/dataset_97245f12-45f9-477c-a596-c33ce24cbf92.dat' '/tmp/tmpz12vnfdi/job_working_directory/000/19/outputs/dataset_f5010fea-0590-4a64-a483-2f1b0b2e3488.dat' '/tmp/tmpz12vnfdi/job_working_directory/000/19/configs/tmproewlyq2' 13 "str,float,float,float,float,float,float,str,int,int,str,str,str" 1
```
**Exit Code:**
* ```console
0
```
**Standard Output:**
* ```console
Filtering with abs(c3)>0.5,
kept 93.75% of 16 valid lines (16 total lines).
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "2770ba06a57011ef9545c98e6440421e" ` |
| chromInfo | ` "/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| cond | ` "abs(c3)>0.5" ` |
| dbkey | ` "?" ` |
| header\_lines | ` "1" ` |
</details>
- **Step 22: join1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
python '/tmp/tmpz12vnfdi/galaxy-dev/tools/filters/join.py' '/tmp/tmpz12vnfdi/files/2/f/8/dataset_2f8a5393-62c6-4052-816b-6ee3379a9676.dat' '/tmp/tmpz12vnfdi/files/f/5/0/dataset_f5010fea-0590-4a64-a483-2f1b0b2e3488.dat' 1 1 '/tmp/tmpz12vnfdi/job_working_directory/000/20/outputs/dataset_d32c0796-1d68-4833-8b87-e033a10dc9c2.dat' --index_depth=3 --buffer=50000000 --fill_options_file=/tmp/tmpz12vnfdi/job_working_directory/000/20/configs/tmpuxq5n2ex -H
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "2770ba06a57011ef9545c98e6440421e" ` |
| chromInfo | ` "/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| field1 | ` "1" ` |
| field2 | ` "1" ` |
| fill\_empty\_columns | ` {"__current_case__": 0, "fill_empty_columns_switch": "no_fill"} ` |
| header | ` "-H" ` |
| partial | ` "" ` |
| unmatched | ` "" ` |
</details>
- **Step 23: Cut1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
perl '/tmp/tmpz12vnfdi/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpz12vnfdi/files/d/3/2/dataset_d32c0796-1d68-4833-8b87-e033a10dc9c2.dat' 'c1-c5' T '/tmp/tmpz12vnfdi/job_working_directory/000/22/outputs/dataset_2b2355c0-e0e8-4403-a1ef-19e5049bcca5.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "tabular" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "2770ba06a57011ef9545c98e6440421e" ` |
| chromInfo | ` "/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| columnList | ` "c1-c5" ` |
| dbkey | ` "?" ` |
| delimiter | ` "T" ` |
</details>
- **Step 24: Generate Heatmap of counts**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cat '/tmp/tmpz12vnfdi/job_working_directory/000/23/configs/tmpoy833em5' && Rscript '/tmp/tmpz12vnfdi/job_working_directory/000/23/configs/tmpoy833em5'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
OS reports request to set locale to "en_US.UTF-8" cannot be honored
Attaching package: ‘gplots’
The following object is masked from ‘package:stats’:
lowess
```
**Standard Output:**
* ```console
options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
library("RColorBrewer")
library("gplots")
input <- read.delim('/tmp/tmpz12vnfdi/files/2/b/2/dataset_2b2355c0-e0e8-4403-a1ef-19e5049bcca5.dat', sep='\t', header=TRUE)
mat_input <- data.matrix(input[,2:ncol(input)])
rownames(mat_input) <- input[,1]
linput <- log2(mat_input+1)
scale <- "none"
srtCol <- 30
rlabs <- FALSE
clabs <- NULL
label_margins <- c(8,1)
dendrogramtoplot <- "both"
reorder_cols <- TRUE
reorder_rows <- TRUE
# Layout is:
# 4 = color key | 3 = dendrogram for columns
# 2 = dendrogram for rows | 1 = heatmap
layout_matrix <- rbind(c(4,3), c(2,1))
key_margins <- list(mar=c(4,0.5,2,1))
lheight <- c(1, 5)
lwidth <- c(1,3)
hclust_fun <- function(x) hclust(x, method='complete')
dist_fun <- function(x) dist(x, method='euclidean')
ncolors <- 50
colused <- colorRampPalette(c("#ffffff", "#ff0000"))(ncolors)
pdf(file='/tmp/tmpz12vnfdi/job_working_directory/000/23/outputs/dataset_321621a0-1792-4d69-b7a7-a408d2b92b0a.dat')
heatmap.2(linput, dendrogram=dendrogramtoplot, Colv=reorder_cols, Rowv=reorder_rows,
distfun=dist_fun, hclustfun=hclust_fun, scale = scale, labRow = rlabs, labCol = clabs,
col=colused, trace="none", density.info = "none", margins=label_margins,
main = '', cexCol=0.8, cexRow=0.8, srtCol=srtCol,
keysize=3, key.xlab='', key.title='', key.par=key_margins,
lmat=layout_matrix, lhei=lheight, lwid=lwidth)
dev.off()
null device
1
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "2770ba06a57011ef9545c98e6440421e" ` |
| chromInfo | ` "/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| cluster\_cond | ` {"__current_case__": 0, "cluster": "yes", "cluster_cols_rows": "both", "clustering": "complete", "distance": "euclidean"} ` |
| colorchoice | ` {"__current_case__": 1, "color1": "#ffffff", "color2": "#ff0000", "type": "two"} ` |
| dbkey | ` "?" ` |
| image\_file\_format | ` "pdf" ` |
| key | ` "" ` |
| labels | ` "columns" ` |
| title | ` "" ` |
| transform | ` "log2plus1" ` |
| zscore\_cond | ` {"__current_case__": 0, "scale": "none", "zscore": "none"} ` |
</details>
- **Step 25: Generate Heatmap of Z-scores**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cat '/tmp/tmpz12vnfdi/job_working_directory/000/24/configs/tmpk3xixofh' && Rscript '/tmp/tmpz12vnfdi/job_working_directory/000/24/configs/tmpk3xixofh'
```
**Exit Code:**
* ```console
0
```
**Standard Error:**
* ```console
Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
OS reports request to set locale to "en_US.UTF-8" cannot be honored
Attaching package: ‘gplots’
The following object is masked from ‘package:stats’:
lowess
```
**Standard Output:**
* ```console
options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
library("RColorBrewer")
library("gplots")
input <- read.delim('/tmp/tmpz12vnfdi/files/2/b/2/dataset_2b2355c0-e0e8-4403-a1ef-19e5049bcca5.dat', sep='\t', header=TRUE)
mat_input <- data.matrix(input[,2:ncol(input)])
rownames(mat_input) <- input[,1]
linput <- mat_input
linput <- t(apply(linput, 1, scale))
colnames(linput) <- colnames(input)[2:ncol(input)]
rownames(linput) <- input[,1]
scale <- "none"
srtCol <- 30
rlabs <- FALSE
clabs <- NULL
label_margins <- c(8,1)
dendrogramtoplot <- "both"
reorder_cols <- TRUE
reorder_rows <- TRUE
# Layout is:
# 4 = color key | 3 = dendrogram for columns
# 2 = dendrogram for rows | 1 = heatmap
layout_matrix <- rbind(c(4,3), c(2,1))
key_margins <- list(mar=c(4,0.5,2,1))
lheight <- c(1, 5)
lwidth <- c(1,3)
hclust_fun <- function(x) hclust(x, method='complete')
dist_fun <- function(x) dist(x, method='euclidean')
ncolors <- 50
colused <- colorRampPalette(c("#0000ff", "#ffffff", "#ff0000"))(ncolors)
pdf(file='/tmp/tmpz12vnfdi/job_working_directory/000/24/outputs/dataset_cdb2d506-529c-4aeb-9759-926ffb34a107.dat')
heatmap.2(linput, dendrogram=dendrogramtoplot, Colv=reorder_cols, Rowv=reorder_rows,
distfun=dist_fun, hclustfun=hclust_fun, scale = scale, labRow = rlabs, labCol = clabs,
col=colused, trace="none", density.info = "none", margins=label_margins,
main = '', cexCol=0.8, cexRow=0.8, srtCol=srtCol,
keysize=3, key.xlab='', key.title='', key.par=key_margins,
lmat=layout_matrix, lhei=lheight, lwid=lwidth)
dev.off()
null device
1
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "2770ba06a57011ef9545c98e6440421e" ` |
| chromInfo | ` "/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| cluster\_cond | ` {"__current_case__": 0, "cluster": "yes", "cluster_cols_rows": "both", "clustering": "complete", "distance": "euclidean"} ` |
| colorchoice | ` {"__current_case__": 2, "color1": "#0000ff", "color2": "#ffffff", "color3": "#ff0000", "type": "three"} ` |
| dbkey | ` "?" ` |
| image\_file\_format | ` "pdf" ` |
| key | ` "" ` |
| labels | ` "columns" ` |
| title | ` "" ` |
| transform | ` "none" ` |
| zscore\_cond | ` {"__current_case__": 1, "zscore": "rows"} ` |
</details>
- **Step 4: Gene Annotaton**:
* step_state: scheduled
- **Step 5: Adjusted p-value threshold**:
* step_state: scheduled
- **Step 6: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_text\_file\_with\_recurring\_lines/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
times=1; yes -- 'GeneID__tc__Base mean__tc__log2(FC)__tc__StdErr__tc__Wald-Stats__tc__P-value__tc__P-adj__tc__Chromosome__tc__Start__tc__End__tc__Strand__tc__Feature__tc__Gene name' 2>/dev/null | head -n $times >> '/tmp/tmpz12vnfdi/job_working_directory/000/6/outputs/dataset_61d0427f-6a80-463f-bbe7-455c45adad70.dat';
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "2770ba06a57011ef9545c98e6440421e" ` |
| chromInfo | ` "/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| token\_set | ` [{"__index__": 0, "line": "GeneID\tBase mean\tlog2(FC)\tStdErr\tWald-Stats\tP-value\tP-adj\tChromosome\tStart\tEnd\tStrand\tFeature\tGene name", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}] ` |
</details>
- **Step 7: log2 fold change threshold**:
* step_state: scheduled
- **Step 8: toolshed.g2.bx.psu.edu/repos/iuc/pick\_value/pick\_value/0.2.0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cd ../; python _evaluate_expression_.py
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "2770ba06a57011ef9545c98e6440421e" ` |
| chromInfo | ` "/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| style\_cond | ` {"__current_case__": 1, "pick_style": "first_or_default", "type_cond": {"__current_case__": 2, "default_value": "0.05", "param_type": "float", "pick_from": [{"__index__": 0, "value": "0.1"}]}} ` |
</details>
- **Step 9: toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_sed\_tool/9.3+galaxy1**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
sed --sandbox -r -f '/tmp/tmpz12vnfdi/job_working_directory/000/8/configs/tmp0wyalgm8' '/tmp/tmpz12vnfdi/files/6/1/d/dataset_61d0427f-6a80-463f-bbe7-455c45adad70.dat' > '/tmp/tmpz12vnfdi/job_working_directory/000/8/outputs/dataset_943262f7-06a4-46a3-b2a9-ca2c09cd6642.dat'
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "2770ba06a57011ef9545c98e6440421e" ` |
| adv\_opts | ` {"__current_case__": 0, "adv_opts_selector": "basic"} ` |
| chromInfo | ` "/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| code | ` "s/__tc__/\\t/g" ` |
| dbkey | ` "?" ` |
</details>
- **Step 10: toolshed.g2.bx.psu.edu/repos/iuc/pick\_value/pick\_value/0.2.0**:
* step_state: scheduled
* <details><summary>Jobs</summary>
- **Job 1:**
* Job state is ok
**Command Line:**
* ```console
cd ../; python _evaluate_expression_.py
```
**Exit Code:**
* ```console
0
```
**Traceback:**
* ```console
```
**Job Parameters:**
* | Job parameter | Parameter value |
| ------------- | --------------- |
| \_\_input\_ext | ` "input" ` |
| \_\_workflow\_invocation\_uuid\_\_ | ` "2770ba06a57011ef9545c98e6440421e" ` |
| chromInfo | ` "/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
| dbkey | ` "?" ` |
| style\_cond | ` {"__current_case__": 1, "pick_style": "first_or_default", "type_cond": {"__current_case__": 2, "default_value": "1.0", "param_type": "float", "pick_from": [{"__index__": 0, "value": "0.5"}]}} ` |
</details>
</details>-
Other invocation details
- **history_id** * 6c1a105ff0beebf7 - **history_state** * ok - **invocation_id** * 6c1a105ff0beebf7 - **invocation_state** * scheduled - **workflow_id** * 6c1a105ff0beebf7
Hello! This is an automated update of the following workflow: workflows/transcriptomics/rnaseq-de. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.
By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2should be updated totoolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3.1+galaxy0should be updated totoolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.2.0+galaxy1The workflow release number has been updated from 0.1 to 0.2.
If you want to skip this change, close this PR without deleting the branch. It will be reopened if another change is detected. Any commit from another author than 'planemo-autoupdate' will prevent more auto-updates. To ignore manual changes and allow autoupdates, delete the branch.