metaQuantome tutorial: part I

[subinamehta]

This tutorial is for uses who want to create datasets that are compatible with the metaQuantome tool. Second part will follow soon.

[subinamehta]

done!

On Sat, Oct 10, 2020 at 4:29 PM Mallory Freeberg notifications@github.com wrote:

@malloryfreeberg commented on this pull request.

In topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md https://github.com/galaxyproject/training-material/pull/2039#discussion_r502829183 :

@@ -0,0 +1,656 @@ +--- +layout: tutorial_hands_on + +title: metaQuantome Data creation tutorial +zenodo_link: '(https://doi.org/10.5281/zenodo.4037137)'

I think the parentheses here are failing the linting check. Suggest changing the line to:

zenodo_link: "https://doi.org/10.5281/zenodo.4037137"

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Subina Mehta Bioinformatics Researcher Dept. of Biochemistry, Molecular Biology and Biophysics University of Minnesota 7-166 MCB 420 Washington Ave SE Minneapolis, MN 55455

Lab: 612-624-0381 Phone: 612-500-8841

Email: smehta@umn.edu smehta@umn.edu www.galaxyp.org http://www.galaxyp.org

[subinamehta]

Done! Please Review!

On Sun, Oct 11, 2020 at 6:34 AM Mallory Freeberg notifications@github.com wrote:

@malloryfreeberg commented on this pull request.

In topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md https://github.com/galaxyproject/training-material/pull/2039#discussion_r502897156 :

+

• 

  +

The linter seems to have issues with how the images are being called out after converting the tutorial.md to html:

• ./_site/training-material/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html
  • image ../../images/microbiome.png does not have an alt attribute (line 444) ...

In other tutorials, images are called out using the following notation:

where CEL-Seq2 Scheme is the alt_text and "Read1 encapsulates the barcodes, and Read2 the mRNA sequence" is inserted as the legend for the figure.

I suggest either:

1. Replacing html-style image call-outs to the markdown style shown above OR
2. Updating existing html-style image call-outs to include alt and title attributes, like:

Maybe one of these options is preferred over the other by the training team?

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Subina Mehta Bioinformatics Researcher Dept. of Biochemistry, Molecular Biology and Biophysics University of Minnesota 7-166 MCB 420 Washington Ave SE Minneapolis, MN 55455

Lab: 612-624-0381 Phone: 612-500-8841

Email: smehta@umn.edu smehta@umn.edu www.galaxyp.org http://www.galaxyp.org

[subinamehta]

Done

On Mon, Oct 12, 2020, 4:20 AM Mallory Freeberg notifications@github.com wrote:

@malloryfreeberg commented on this pull request.

In topics/proteomics/tutorials/metaquantome-data-creation/workflows/main_workflow.ga https://github.com/galaxyproject/training-material/pull/2039#discussion_r503119082 :

@@ -0,0 +1,1116 @@

+{

• "a_galaxy_workflow": "true",

• "annotation": "",

@subinamehta https://github.com/subinamehta This should be the last change to make to get the linter to pass 👍

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[subinamehta]

made those changes

On Mon, Oct 12, 2020 at 3:17 PM Mallory Freeberg notifications@github.com wrote:

@malloryfreeberg commented on this pull request.

In topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md https://github.com/galaxyproject/training-material/pull/2039#discussion_r503486098 :

+> +> 1. TOC +> {:toc} +> +{: .agenda} + +# Pretreatments + +The first step in a tutorial is to get the data from the zenodo link provided and making sure that it is in the correct format. + +## Get data + +> ### {% icon hands_on %} Hands-on: Data upload +> +> 1. Create a new history for this tutorial +> 2. Import the files ( 6 MZML files, a Protein FASTA file and Experimental Design file) from [Zenodo]({{ page.zenodo_link }})

I suggest specifically confirming what the datatypes/formats of the files should be.

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Subina Mehta Bioinformatics Researcher Dept. of Biochemistry, Molecular Biology and Biophysics University of Minnesota 7-166 MCB 420 Washington Ave SE Minneapolis, MN 55455

Lab: 612-624-0381 Phone: 612-500-8841

Email: smehta@umn.edu smehta@umn.edu www.galaxyp.org http://www.galaxyp.org

[malloryfreeberg]

Hi @subinamehta

When I try to run the msconvert step in the "Hands-on: mzml to MGF" section, I get the following error:

"No pepxml or mzid dataset available." Can you let me know if I'm missing something here or if there is a mistake? Thanks!

[subinamehta]

I dont have that version of msconvert, mine looks something like this.

On Mon, Oct 12, 2020 at 3:38 PM Mallory Freeberg notifications@github.com wrote:

Hi @subinamehta https://github.com/subinamehta

When I try to run the msconvert step in the "Hands-on: mzml to MGF" section, I get the following error:

[image: Screenshot 2020-10-12 at 20 33 09] https://user-images.githubusercontent.com/10993501/95783707-4d9d1780-0cca-11eb-8b3e-ff7ccf358c89.png

"No pepxml or mzid dataset available." Can you let me know if I'm missing something here or if there is a mistake? Thanks!

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Subina Mehta Bioinformatics Researcher Dept. of Biochemistry, Molecular Biology and Biophysics University of Minnesota 7-166 MCB 420 Washington Ave SE Minneapolis, MN 55455

Lab: 612-624-0381 Phone: 612-500-8841

Email: smehta@umn.edu smehta@umn.edu www.galaxyp.org http://www.galaxyp.org

[malloryfreeberg]

Hi @subinamehta

Thanks for being so responsive to all my suggestions 👍

A few more comments/suggestions:

1. I am trying to follow the tutorial using https://usegalaxy.eu/. When setting "Apply m/z refinement with identification data?" to "yes", the msconvert tool (Galaxy Version 3.0.19052.1) requires an input file to "MZRefinery - Input identification data". Can you please advise whether 1) this file needs to be added to the history, 2) a different version of the tool needs to be used, or 3) if there is an alternate or custom Galaxy I should be using to test this tutorial.
2. I suggest making sure there is a title after each "Hands-on:" tag.
3. I suggest that for all tool parameters which require a dataset or collection as input, remove specific names of input files to various tools. Users will have different dataset names, so it's more clear to describe which dataset should be chosen as input. For example, instead of: “Tabular Input Containing Peptide column”: `out_file1` (output of Filter tool) I suggest using: “Tabular Input Containing Peptide column”: Select output of Filter tool

[subinamehta]

Thanks for helping me refine my tutorial. I will make these changes today. For msconvert I checked it this way- msconvert Convert and/or filter mass spectrometry files (Galaxy Version 3.0.19052.1) Apply m/z refinement with identification data? YesNo

On Mon, Oct 12, 2020 at 4:43 PM Mallory Freeberg notifications@github.com wrote:

Hi @subinamehta https://github.com/subinamehta

Thanks for being so responsive to all my suggestions 👍

A few more comments/suggestions:

1. I am trying to follow the tutorial using https://usegalaxy.eu/. When setting "Apply m/z refinement with identification data?" to "yes", the msconvert tool (Galaxy Version 3.0.19052.1) requires an input file to "MZRefinery - Input identification data". Can you please advise whether 1) this file needs to be added to the history, 2) a different version of the tool needs to be used, or 3) if there is an alternate or custom Galaxy I should be using to test this tutorial.
2. I suggest making sure there is a title after each "Hands-on:" tag.
3. I suggest that for all tool parameters which require a dataset or collection as input, remove specific names of input files to various tools. Users will have different dataset names, so it's more clear to describe which dataset should be chosen as input. For example, instead of: “Tabular Input Containing Peptide column”: out_file1 (output of Filter tool) I suggest using: “Tabular Input Containing Peptide column”: Select output of Filter tool

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Subina Mehta Bioinformatics Researcher Dept. of Biochemistry, Molecular Biology and Biophysics University of Minnesota 7-166 MCB 420 Washington Ave SE Minneapolis, MN 55455

Lab: 612-624-0381 Phone: 612-500-8841

Email: smehta@umn.edu smehta@umn.edu www.galaxyp.org http://www.galaxyp.org

[subinamehta]

Made all the required changes!

On Mon, Oct 12, 2020 at 4:48 PM Subina Mehta smehta@umn.edu wrote:

Thanks for helping me refine my tutorial. I will make these changes today. For msconvert I checked it this way- msconvert Convert and/or filter mass spectrometry files (Galaxy Version 3.0.19052.1) Apply m/z refinement with identification data? YesNo

On Mon, Oct 12, 2020 at 4:43 PM Mallory Freeberg notifications@github.com wrote:

Hi @subinamehta https://github.com/subinamehta

Thanks for being so responsive to all my suggestions 👍

A few more comments/suggestions:

1. I am trying to follow the tutorial using https://usegalaxy.eu/. When setting "Apply m/z refinement with identification data?" to "yes", the msconvert tool (Galaxy Version 3.0.19052.1) requires an input file to "MZRefinery - Input identification data". Can you please advise whether 1) this file needs to be added to the history, 2) a different version of the tool needs to be used, or 3) if there is an alternate or custom Galaxy I should be using to test this tutorial.
2. I suggest making sure there is a title after each "Hands-on:" tag.
3. I suggest that for all tool parameters which require a dataset or collection as input, remove specific names of input files to various tools. Users will have different dataset names, so it's more clear to describe which dataset should be chosen as input. For example, instead of: “Tabular Input Containing Peptide column”: out_file1 (output of Filter tool) I suggest using: “Tabular Input Containing Peptide column”: Select output of Filter tool

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Subina Mehta Bioinformatics Researcher Dept. of Biochemistry, Molecular Biology and Biophysics University of Minnesota 7-166 MCB 420 Washington Ave SE Minneapolis, MN 55455

Lab: 612-624-0381 Phone: 612-500-8841

Email: smehta@umn.edu smehta@umn.edu www.galaxyp.org http://www.galaxyp.org

--

Subina Mehta Bioinformatics Researcher Dept. of Biochemistry, Molecular Biology and Biophysics University of Minnesota 7-166 MCB 420 Washington Ave SE Minneapolis, MN 55455

Lab: 612-624-0381 Phone: 612-500-8841

Email: smehta@umn.edu smehta@umn.edu www.galaxyp.org http://www.galaxyp.org

[subinamehta]

Made the required changes.

On Tue, Oct 13, 2020 at 6:47 AM Saskia Hiltemann notifications@github.com wrote:

@shiltemann commented on this pull request.

In topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md https://github.com/galaxyproject/training-material/pull/2039#discussion_r503851928 :

+{: .agenda} + +# Pretreatments + +The first step in a tutorial is to get the data from the zenodo link provided and making sure that it is in the correct format. + +## Get data + +> ### {% icon hands_on %} Hands-on: Data upload +> +> 1. Create a new history for this tutorial and give it a meaningful name +> +> {% include snippets/create_new_history.md %} +> {% include snippets/rename_history.md %} +> +> 2. Import the files: 6 MZML files (format=mzml, a Protein FASTA file (format=fasta), and an Experimental Design file (format=tabular) from [Zenodo]({{ page.zenodo_link }})

the format information might be nicer to put in step 4 below?

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Subina Mehta Bioinformatics Researcher Dept. of Biochemistry, Molecular Biology and Biophysics University of Minnesota 7-166 MCB 420 Washington Ave SE Minneapolis, MN 55455

Lab: 612-624-0381 Phone: 612-500-8841

Email: smehta@umn.edu smehta@umn.edu www.galaxyp.org http://www.galaxyp.org

[subinamehta]

done

On Tue, Oct 13, 2020 at 2:08 PM Mallory Freeberg notifications@github.com wrote:

@malloryfreeberg commented on this pull request.

In topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md https://github.com/galaxyproject/training-material/pull/2039#discussion_r504156023 :

+ +# Conclusion +{:.no_toc} + +This completes the walkthrough of the metaQuantome data creation workflow .This tutorial is a guide to have datasets that are metaQuantome ready/compatible and can be used for metaproteomics research. We have incorporated only two conditions in this workflow but users can use as many as they want. Researchers can use this workflow with their data also, please make sure the tool parameters and the workflow will be needed to be modified accordingly. + +Please look at the following tutorials in this Metaproteomics series: + +[Metaproteomics]({% link topics/proteomics/tutorials/metaproteomics/tutorial.md %}) +This workflow is also available at proteomics.usegalaxy.eu + +This workflow was developed by the Galaxy-P team at the University of Minnesota. For more information about Galaxy-P or our ongoing work, please visit us at galaxyp.org + +> ### {% icon comment %} References +> +> - {% Batut2018 %}

Need to add cite at the beginning of all the citation blocks here. This should allow the linter to pass.

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Subina Mehta Bioinformatics Researcher Dept. of Biochemistry, Molecular Biology and Biophysics University of Minnesota 7-166 MCB 420 Washington Ave SE Minneapolis, MN 55455

Lab: 612-624-0381 Phone: 612-500-8841

Email: smehta@umn.edu smehta@umn.edu www.galaxyp.org http://www.galaxyp.org

[subinamehta]

Was that a space issue?

On Tue, Oct 13, 2020 at 3:16 PM Mallory Freeberg notifications@github.com wrote:

@malloryfreeberg commented on this pull request.

In topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md https://github.com/galaxyproject/training-material/pull/2039#discussion_r504196620 :

+> {% include snippets/import_via_link.md %} +> {% include snippets/import_from_data_library.md %} +> +> +> 3. Rename the datasets (If needed) +> 4. Check that the datatype ( Make sure they are in the correct formats). +> 6 MZML files (format=mzml, a Protein FASTA file (format=fasta), and an Experimental Design file (format=tabular) +> +> {% include snippets/change_datatype.md datatype="datatypes" %} +> +> 5. Add to each database a tag corresponding to the name of the input data (optional). +> 6. Build a Dataset list for the four mzml files. +> - Click the Operations on multiple datasets check box at the top of the history panel +> +> +> {% include snippets/create_dataset_collection.md datatype="collection" %}

This will fix the incorrect indentation here.

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Subina Mehta Bioinformatics Researcher Dept. of Biochemistry, Molecular Biology and Biophysics University of Minnesota 7-166 MCB 420 Washington Ave SE Minneapolis, MN 55455

Lab: 612-624-0381 Phone: 612-500-8841

Email: smehta@umn.edu smehta@umn.edu www.galaxyp.org http://www.galaxyp.org

[malloryfreeberg]

Was that a space issue?

Yes, before there were 2 spaces between the > and the number, which meant the number wasn't interpreted as a number in the automatic numbering (and therefore there were two #1s), and the indentation of the tips wasn't correct:

But with only 1 space between the > and the number, it is now recognised as a number and the Tips are indented correctly:

[subinamehta]

I fixed it now

On Tue, Oct 13, 2020 at 3:25 PM Mallory Freeberg notifications@github.com wrote:

Was that a space issue?

Yes, before there were 2 spaces between the > and the number, which meant the number wasn't interpreted as a number in the automatic numbering (and therefore there were two #1s), and the indentation of the tips wasn't correct:

[image: incorrect-numbering] https://user-images.githubusercontent.com/10993501/95906485-172acf80-0d92-11eb-8dc5-a44e9d2ed547.png

But with only 1 space between the > and the number, it is now recognised as a number and the Tips are indented correctly:

[image: correct-numbering] https://user-images.githubusercontent.com/10993501/95906347-eba7e500-0d91-11eb-9926-75fe8b6b7c0a.png

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Subina Mehta Bioinformatics Researcher Dept. of Biochemistry, Molecular Biology and Biophysics University of Minnesota 7-166 MCB 420 Washington Ave SE Minneapolis, MN 55455

Lab: 612-624-0381 Phone: 612-500-8841

Email: smehta@umn.edu smehta@umn.edu www.galaxyp.org http://www.galaxyp.org

[malloryfreeberg]

Hi @subinamehta

Great work so far! 👍

I still am unable to run the tutorial from start to finish successfully on a public Galaxy instance. I have tried:

1. Running on Galaxy Metaproteomics Instance (z.umn.edu/metaproteomicsgateway). When I try to import the workflow, I get the error message: "Following tools missing: toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.0, toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0". The workflow doesn't import so I can't run it.

2. Running on Galaxy Europe. I can import and run the workflow, but the FlashLFQ steps all fail with errors: "parameter 'ctr': an invalid option ('S1') was selected (valid options: GMGMDTKELVLKVLKESEEPLRPGQIAEKANIDKKEVDKAIKELKKEDLIESPKRCFYTAK,MKSKIYFADARAKAYDFKYSFVAKFEQILDMIDFKQFISKKDYVAIKTHFGSYGAHRIVRPIFLKKVVDKVKEVGGKPFVTDTVRIPGLEYLDVANMEGINHLSVGAPVILADGIFGRDSIK". Also, the Regex Find And Replace tool cannot run because it depends on the output of FlashLFQ. There are no instructions for how to fix this error.

3. Running on Galaxy Main. Same as Galaxy Metaproteomics Instance; some of the tools are missing so the workflow won't import.

4. Running on Galaxy Australia. Same as Galaxy Metaproteomics Instance and Galaxy Main; some of the tools are missing so the workflow won't import.

@shiltemann I'm not sure what the GTN policy is here regarding where a tutorial workflow should be able to be run. Can you please advise? I don't want to approve this PR until I can successfully run the workflow somewhere.

Thanks!

[subinamehta]

z.metaproteomicsgateway is going to be closed soon...I am not sure about Galaxy Main n Australia because I haven't used them. But the workflow works on Galaxy eu for me and others in our group and our collaborators. If you could share the history with me..It could help me figure out the issue. Also peptides cannot be used as a control for FlashLFQ. In the experimental design file I have mentioned S1 and S2 are the conditions.

On Tue, Oct 13, 2020 at 4:17 PM Mallory Freeberg notifications@github.com wrote:

Hi @subinamehta https://github.com/subinamehta

Great work so far! 👍

I still am unable to run the tutorial from start to finish successfully on a public Galaxy instance. I have tried:

1.

Running on Galaxy Metaproteomics Instance ( z.umn.edu/metaproteomicsgateway). When I try to import the workflow, I get the error message: "Following tools missing: toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.0, toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0". The workflow doesn't import so I can't run it. 2.

Running on Galaxy Europe. I can import and run the workflow, but the FlashLFQ steps all fail with errors: "parameter 'ctr': an invalid option ('S1') was selected (valid options: GMGMDTKELVLKVLKESEEPLRPGQIAEKANIDKKEVDKAIKELKKEDLIESPKRCFYTAK,MKSKIYFADARAKAYDFKYSFVAKFEQILDMIDFKQFISKKDYVAIKTHFGSYGAHRIVRPIFLKKVVDKVKEVGGKPFVTDTVRIPGLEYLDVANMEGINHLSVGAPVILADGIFGRDSIK". Also, the Regex Find And Replace tool cannot run because it depends on the output of FlashLFQ. There are no instructions for how to fix this error. 3.

Running on Galaxy Main. Same as Galaxy Metaproteomics Instance; some of the tools are missing so the workflow won't import. 4.

Running on Galaxy Australia. Same as Galaxy Metaproteomics Instance and Galaxy Main; some of the tools are missing so the workflow won't import.

@shiltemann https://github.com/shiltemann I'm not sure what the GTN policy is here regarding where a tutorial workflow should be able to be run. Can you please advise? I don't want to approve this PR until I can successfully run the workflow somewhere.

Thanks!

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Subina Mehta Bioinformatics Researcher Dept. of Biochemistry, Molecular Biology and Biophysics University of Minnesota 7-166 MCB 420 Washington Ave SE Minneapolis, MN 55455

Lab: 612-624-0381 Phone: 612-500-8841

Email: smehta@umn.edu smehta@umn.edu www.galaxyp.org http://www.galaxyp.org

[shiltemann]

@malloryfreeberg thanks for your thorough review!! If we can get this working on at leaset GalaxyEU it should be good enough.

I uploaded the files and the tutorial .ga file to GalaxyEU, and it seemed to complete without error for me (history: https://usegalaxy.eu/u/saskia/h/metaquantome). Could you double check that the correct file was used as the design file? (The workflow run menu did not auto-pick the right option for me, I had to manually change it to the correct one)

[subinamehta]

Made the require changes with references...the workflow still works for me!

[malloryfreeberg]

Hi @shiltemann and @subinamehta

I had indeed not changed from the auto-selected design file to the real one. After doing so, the workflow worked for me on Galaxy Europe! 🎉

I'm working through the tutorial manually now, and I'm not sure what I'm supposed to select for parameters to the Search GUI like the following:

Can you advise whether the user is meant to select or unselect these parameters? Maybe it would be more clear to directly specify "Select" or "Unselect", something like:

[subinamehta]

Apologies for not checking that earlier..made those changes..don't know why it didn't take options when the tutorial was created using the workflow.

On Wed, Oct 14, 2020 at 3:56 PM Mallory Freeberg notifications@github.com wrote:

Hi @shiltemann https://github.com/shiltemann and @subinamehta https://github.com/subinamehta

I had indeed not changed from the auto-selected design file to the real one. After doing so, the workflow worked for me on Galaxy Europe! 🎉

I'm working through the tutorial manually now, and I'm not sure what I'm supposed to select for parameters to the Search GUI like the following:

[image: Screenshot 2020-10-14 at 20 30 12] https://user-images.githubusercontent.com/10993501/96036913-0dba6980-0e5d-11eb-9ea6-65de9b5ff9a6.png

Can you advise whether the user is meant to select or unselect these parameters? Maybe it would be more clear to directly specify "Select" or "Unselect", something like:

[image: Screenshot 2020-10-14 at 20 53 57] https://user-images.githubusercontent.com/10993501/96038806-9df9ae00-0e5f-11eb-97ab-21681af95a1b.png

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Subina Mehta Bioinformatics Researcher Dept. of Biochemistry, Molecular Biology and Biophysics University of Minnesota 7-166 MCB 420 Washington Ave SE Minneapolis, MN 55455

Lab: 612-624-0381 Phone: 612-500-8841

Email: smehta@umn.edu smehta@umn.edu www.galaxyp.org http://www.galaxyp.org

[malloryfreeberg]

Thanks @subinamehta!

Can you please go through the tutorial and update the other parameters that this happened to? I can see at least 5 other parameters that show ``. Thanks! 👍

[subinamehta]

My gosh..i need a spellcheck

On Thu, Oct 15, 2020 at 10:08 AM Saskia Hiltemann notifications@github.com wrote:

@shiltemann commented on this pull request.

In topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md https://github.com/galaxyproject/training-material/pull/2039#discussion_r505572964 :

+ +> ### {% icon hands_on %} Hands-on: Remove # from peptide header +> 1. {% tool Replace Text %} with the following parameters: +> - {% icon param-file %} "File to process": Unipept_Function (output of Unipept {% icon tool %}) +> - In "Replacement": +> - {% icon param-repeat %} "Insert Replacement" +> - "Find pattern": #peptide +> - "Replace with:": peptide +> +> 2. Rename file as All_functions +{: .hands_on} + + +## Filter - EC values + +We are using this Query tabular ot rename the output that we obtained from the Cut column tool.

ot -> to?

And I guess this tool does more than rename output from the cut tool? maybe have a look at this?

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Subina Mehta Bioinformatics Researcher Dept. of Biochemistry, Molecular Biology and Biophysics University of Minnesota 7-166 MCB 420 Washington Ave SE Minneapolis, MN 55455

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Email: smehta@umn.edu smehta@umn.edu www.galaxyp.org http://www.galaxyp.org

[malloryfreeberg]

I'm following the "Hands-on: Interpretation of Search GUI" step, which instructs to set: "Compress results into a single zip file": Yes:

However, when I run the tool with this parameter, there is only one output produced that is a zipped dataset:

And I can't select any individual reports for the next two "Select" steps. When I check what parameters were used when I ran the workflow, I see that the parameter is set to: "Compress results into a single zip file": No:

Also, in the workflow only 4 reports are selected to be generated instead of all reports (as shown in the tutorial).

Please update this step in the tutorial to be sure that usable datasets are produced. I suspect you can either set "Compress results into a single zip file" and "Also export reports out of the zip" parameters both to Yes or set both to No to make sure the individual reports are generated in the history.

[subinamehta]

I dont think that should be right..the input is mzml..if that is then it is a problem

On Thu, Oct 15, 2020 at 3:16 PM Mallory Freeberg notifications@github.com wrote:

@malloryfreeberg commented on this pull request.

In topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md https://github.com/galaxyproject/training-material/pull/2039#discussion_r505781231 :

+>

+{: .question}

+

+

+## Removing file extensions for Quantification

+This is a data manipulation step to make the data compatible with other downstream processing tools. The Replace text tool replaces the .mgf extension from the PSM report so that it can be used as an input for FlashLFQ.

+>

+> ### {% icon hands_on %} Hands-on: Removing file extensions

+>

+>

+> 1. {% tool Replace Text %} with the following parameters:

+> - {% icon param-file %} "File to process": PSM_Report_no_contaminants (output of Select {% icon tool %})

+> - In "Replacement":

+> - {% icon param-repeat %} "Insert Replacement"

+> - "in column": c10

+> - "Find pattern": .mzml.mgf

⬇️ Suggested change

-> - "Find pattern": .mzml.mgf

+> - "Find pattern": .raw.mgf

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Subina Mehta Bioinformatics Researcher Dept. of Biochemistry, Molecular Biology and Biophysics University of Minnesota 7-166 MCB 420 Washington Ave SE Minneapolis, MN 55455

Lab: 612-624-0381 Phone: 612-500-8841

Email: smehta@umn.edu smehta@umn.edu www.galaxyp.org http://www.galaxyp.org

[malloryfreeberg]

I dont think that should be right..the input is mzml..if that is then it is a problem

Weird. This is what I see when I look at my history from running the workflow (which was successful):

[subinamehta]

I dont think that should be right..the input is mzml..if that is then it is a problem

Weird. This is what I see when I look at my history from running the workflow (which was successful):

Yeah..it ran but FlashLFQ might have given empty output... I made changes to the workflow..It was a WIP when the tutorial was created..so I think I didnt realize that there was an error in the replace expression..Thankyou for catching this.

[malloryfreeberg]

Yeah..it ran but FlashLFQ might have given empty output... I made changes to the workflow..It was a WIP when the tutorial was created..so I think I didnt realize that there was an error in the replace expression..Thankyou for catching this.

Thanks for the explanation. I'll re-run the updated workflow and continue working through the tutorial step-by-step as well.

[malloryfreeberg]

Hi @subinamehta

The tutorial is great! 🎉 🎉 🎉 It's clear a lot of work went into creating it, so kudos to you and all the other contributors for a job well done.

The last thing to look at is the newest version of the workflow. After running it, a few of the datasets are empty: items 27, 30, and 34 in this history.

Just want to check whether this was expected, or if the workflow needs adjusted. I think this is the last change before merging!

[subinamehta]

Done! In the workflow, it was written.mzML rather than .mzml..so the regex never happened... I reran the tools with the changes and it worked..I fixed the workflow also...

https://usegalaxy.eu/u/subina/h/imported-metaquantome-data-creation-tutorial-workflow---v2

On Thu, Oct 15, 2020 at 6:04 PM Mallory Freeberg notifications@github.com wrote:

Hi @subinamehta https://github.com/subinamehta

The tutorial is great! 🎉 🎉 🎉 It's clear a lot of work went into creating it, so kudos to you and all the other contributors for a job well done.

The last thing to look at is the newest version of the workflow. After running it, a few of the datasets are empty: items 27, 30, and 34 in this history https://usegalaxy.eu/u/ef57a2de41414feea0dc0ddfedf02a9d/h/metaquantome-data-creation-tutorial-workflow-v2 .

Just want to check whether this was expected, or if the workflow needs adjusted. I think this is the last change before merging!

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Subina Mehta Bioinformatics Researcher Dept. of Biochemistry, Molecular Biology and Biophysics University of Minnesota 7-166 MCB 420 Washington Ave SE Minneapolis, MN 55455

Lab: 612-624-0381 Phone: 612-500-8841

Email: smehta@umn.edu smehta@umn.edu www.galaxyp.org http://www.galaxyp.org

[shiltemann]

awesome, thanks @subinamehta and team! And thanks @malloryfreeberg for the great review! :tada:

[subinamehta]

Thanks to you both Saskia and Mallory for your help on making this possible!!! Time to work on the next one!

On Fri, Oct 16, 2020 at 8:56 AM Saskia Hiltemann notifications@github.com wrote:

awesome, thanks @subinamehta https://github.com/subinamehta and team! And thanks @malloryfreeberg https://github.com/malloryfreeberg for the great review! 🎉

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Subina Mehta Bioinformatics Researcher Dept. of Biochemistry, Molecular Biology and Biophysics University of Minnesota 7-166 MCB 420 Washington Ave SE Minneapolis, MN 55455

Lab: 612-624-0381 Phone: 612-500-8841

Email: smehta@umn.edu smehta@umn.edu www.galaxyp.org http://www.galaxyp.org