Open mvdbeek opened 7 months ago
This should be txt for the datatype, and might be confused with <param type="text"/> maybe ?
txt
<param type="text"/>
tools/stress_ng/stress_ng.xml:851: <!-- <param argument="-\-job" type="data" format="text" --> tools/EDeN/pyeden/predict.xml:20: <data format="text" name="ofile_predictions" from_work_dir="predictions" label="${tool.name} on ${on_string}: Predictions"/> tools/EDeN/pyeden/predict.xml:21: <data format="text" name="ofile_margins" from_work_dir="margins" label="${tool.name} on ${on_string}: Margins"/> tools/EDeN/pyeden/features.xml:20: <data format="text" name="ofile_predictions" from_work_dir="features" label="${tool.name} on ${on_string}: Features"/> tools/EDeN/pyeden/cluster_dbscan.xml:29: <data format="text" name="ofile_vectorizer" from_work_dir="vectorizer" label="${tool.name} on ${on_string}: Vectorizer"/> tools/EDeN/pyeden/cluster_dbscan.xml:30: <data format="text" name="ofile_labels" from_work_dir="labels" label="${tool.name} on ${on_string}: Labels"/> tools/EDeN/pyeden/nearest_neighbor.xml:31: <data format="text" name="ofile_matrix" from_work_dir="matrix" label="${tool.name} on ${on_string}"/> tools/EDeN/pyeden/cluster_kmeans.xml:28: <data format="text" name="ofile_vectorizer" from_work_dir="vectorizer" label="${tool.name} on ${on_string}: Vectorizer"/> tools/EDeN/pyeden/cluster_kmeans.xml:29: <data format="text" name="ofile_labels" from_work_dir="labels" label="${tool.name} on ${on_string}: Labels"/> tools/EDeN/pyeden/fit.xml:34: <data format="text" name="ofile_vectorizer" from_work_dir="vectorizer" label="${tool.name} on ${on_string}: Vectorizer"/> tools/EDeN/pyeden/fit.xml:35: <data format="text" name="ofile_model" from_work_dir="model" label="${tool.name} on ${on_string}: Model"/> tools/EDeN/pyeden/matrix.xml:49: <data format="text" name="ofile_matrix" from_work_dir="matrix" label="${tool.name} on ${on_string}: Matrix"/> tools/EDeN/pyeden/dendogram.xml:47: <data format="text" name="ofile_linkage_matrix" from_work_dir="linkage_matrix" label="${tool.name} on ${on_string}: Linkage Matrix"/> tools/gfastats/gfastats.xml:113: format="text" label="SAK input file" optional="true" tools/gfastats/gfastats.xml:202: <when input="tabular" value="false" format="text"/> tools/sambamba/sambamba_depth.xml:69: <data name="output" format="text"/> tools/sambamba/Sambamba_view.xml:28: <data name="output" format="text"/> tools/openms/InspectAdapter.xml:199: <param name="param_inspect_input" type="data" format="text" label="name for the input file of Inspect (may only be used in a full run)" help="(-inspect_input) "/> tools/openms/MascotAdapter.xml:130: <param name="param_in" type="data" format="text" label="input file in mzData format" help="(-in) <br>Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read"/> tools/openms/TICCalculator.xml:50: <data name="param_stdout" format="text" label="Output from stdout"/> tools/openms/TopPerc.xml:163: <param name="param_percolator_executable" type="data" format="text" label="Path to the percolator binary" help="(-percolator_executable) "/> tools/openms/TopPerc.xml:183: <param name="param_k" type="data" format="text" label="Input file given in the deprecated pin-xml format generated by" help="(-k) e.g. sqt2pin with the -k option"/> tools/openms/TopPerc.xml:184: <param name="param_W" type="data" format="text" label="Read initial weights to the given file" help="(-W) "/> tools/openms/OpenSwathWorkflow.xml:362: <param name="param_swath_windows_file" type="data" format="text" label="Optional, tab separated file containing the SWATH windows for extraction: lower_offset upper_offset \newline 400 425 \newline .." help="(-swath_windows_file) Note that the first line is a header and will be skipped"/> tools/openms/MetaProSIP.xml:121: <param name="param_r_executable" type="data" format="text" value="R" label="Path to the R executable (default: 'R')" help="(-r_executable) "/> tools/openms/MzMLSplitter.xml:67: <data name="param_stdout" format="text" label="Output from stdout"/> tools/openms/OpenSwathFileSplitter.xml:51: <data name="param_stdout" format="text" label="Output from stdout"/> tools/openms/LabeledEval.xml:44: <data name="param_stdout" format="text" label="Output from stdout"/> tools/openms/MapAlignmentEvaluation.xml:65: <data name="param_stdout" format="text" label="Output from stdout"/> tools/openms/InternalCalibration.xml:100: <param name="param_rscript_executable" type="data" format="text" value="Rscript" label="Path to the Rscript executable (default: 'Rscript')" help="(-rscript_executable) "/> tools/openms/XMLValidator.xml:36: <data name="param_stdout" format="text" label="Output from stdout"/> tools/openms/SemanticValidator.xml:48: <data name="param_stdout" format="text" label="Output from stdout"/> tools/openms/FuzzyDiff.xml:66: <param name="param_in1" type="data" format="text" label="first input file" help="(-in1) "/> tools/openms/FuzzyDiff.xml:67: <param name="param_in2" type="data" format="text" label="second input file" help="(-in2) "/> tools/openms/FuzzyDiff.xml:98: <data name="param_stdout" format="text" label="Output from stdout"/> tools/openms/DTAExtractor.xml:76: <data name="param_stdout" format="text" label="Output from stdout"/> tools/biopython/converters/sequence_converter.xml:59: <data format="text" name="outfile" /> tools/genome_annotation_pipeline/eukaryotic_ncbi_submission.xml:82: <param name="trainingset" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset."> tools/augustus/augustus.xml:94: <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset."> tools/staging_area/blast_annotaion_from_genbank.xml:6: <param name="input_genbank_file" type="data" format="text" label="Genbank File"/> tools/staging_area/terpen_finder/terpen_finder.xml:20: <param name="key_name" type="text" format="text" label="Compound Identifier encoded in the SDF-File." help="Specify the key name of the SDF metadata, that contains the molecule identifier."/> tools/staging_area/terpen_finder/terpen_finder.xml:26: <data name="output" format="text" /> tools/staging_area/circos/tools/circos/circosConfigFileCreatorWrapper.xml:147: <param name="imageBackgroundColor" type="select" format="text"> tools/staging_area/circos/tools/circos/circosConfigFileCreatorWrapper.xml:165: <param name="plot_type" type="select" format="text"> tools/staging_area/circos/tools/circos/circosConfigFileCreatorWrapper.xml:179: <param name="plot_color" label='Color' type="select" format="text" multiple='true'> tools/staging_area/circos/tools/circos/circosConfigFileCreatorWrapper.xml:188: <param name="plot_fill_color" label='Fill Color' type="select" format="text" multiple='true'> tools/staging_area/circos/tools/circos/circosConfigFileCreatorWrapper.xml:198: <param name="plot_orientation" label='orientation' type="select" format="text"> tools/staging_area/circos/tools/circos/circosConfigFileCreatorWrapper.xml:208: <param name="plot_axis_color" label='Color' type="select" format="text"> tools/staging_area/circos/tools/circos/circosConfigFileCreatorWrapper.xml:223: <param name="plot_link_color" label='Link Color' type="select" format="text" multiple='true'> tools/staging_area/circos/tools/circos/circosConfigFileCreatorWrapper.xml:233: <param name="plot_label_font" label='Label Font' type="select" format="text" > tools/staging_area/circos/tools/circos/circosConfigFileCreatorWrapper.xml:252: <param name="plot_rule_color" label='Rule Color' type="select" format="text" multiple='true'> tools/staging_area/circos/tools/circos/circosWrapper.xml:148: <param name="imageBackgroundColor" type="select" format="text" label='image background color' help='the image background color'> tools/staging_area/circos/tools/circos/circosWrapper.xml:166: <param name="plot_type" type="select" format="text"> tools/staging_area/circos/tools/circos/circosWrapper.xml:180: <param name="plot_color" label='Color' type="select" format="text" multiple='true' help='the plot color'> tools/staging_area/circos/tools/circos/circosWrapper.xml:189: <param name="plot_fill_color" label='Fill Color' type="select" format="text" multiple='true' help='the plot fill color'> tools/staging_area/circos/tools/circos/circosWrapper.xml:199: <param name="plot_orientation" label='orientation' type="select" format="text"> tools/staging_area/circos/tools/circos/circosWrapper.xml:209: <param name="plot_axis_color" label='Color' type="select" format="text" help='the plot axis color'> tools/staging_area/circos/tools/circos/circosWrapper.xml:224: <param name="plot_link_color" label='Link Color' type="select" format="text" multiple='true' help='the plot link color'> tools/staging_area/circos/tools/circos/circosWrapper.xml:234: <param name="plot_label_font" label='Label Font' type="select" format="text" > tools/staging_area/circos/tools/circos/circosWrapper.xml:253: <param name="plot_rule_color" label='Rule Color' type="select" format="text" multiple='true' help='the rule color'> tools/staging_area/ripcalWrapper.xml:15: <param name='analysis_type' type="select" format="text" label='analysis type'> tools/staging_area/ripcalWrapper.xml:21: <param name='model' type="select" format="text" label='model'> tools/rna_tools/infernal/cmalign.xml:177: <data name="outfile" format="text" label="cmalign on ${on_string}"/> tools/rna_tools/rnaz/rnazRandomizeAln.xml:14: <param type="data" name="input" format="text" /> tools/rna_tools/rnaz/rnazCluster.xml:16: <param type="data" name="input" format="text" /> tools/rna_tools/locarna/locarna_multiple.xml:86: <param name="input_data" type="data" format="text" label="Sequence input" chemicaltoolbox/openbabel/ob_grep.xml:49: <param name="smarts_pattern" type="text" format="text" label="SMARTS Pattern" help="Specify a SMARTS Pattern for your search."/> chemicaltoolbox/openbabel/change_title_to_metadata_value.xml:20: <param name="key" type="text" format="text" label="Compound identifier encoded in the SD-file." help="Specify the key name of the SDF metadata which contains the molecule identifier (e.g. 'PUBCHEM_SHAPE_VOLUME')"/> chemicaltoolbox/openbabel/ob_convert.xml:430: <data name="outfile" format="text" label="Convert to ${oformat.oformat_opts_selector} from ${on_string}">
This should be
txtfor the datatype, and might be confused with<param type="text"/>maybe ?