| Previous changeset 52:864bd76db767 (2019-01-16) Next changeset 54:7fdd9119cc4f (2020-02-20) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 |
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modified:
peptide_shaker.xml |
| b |
| diff -r 864bd76db767 -r d67a3c1bfd09 peptide_shaker.xml --- a/peptide_shaker.xml Wed Jan 16 08:18:39 2019 -0500 +++ b/peptide_shaker.xml Wed May 08 14:06:07 2019 -0400 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="peptide_shaker" name="Peptide Shaker" version="@PEPTIDESHAKER_VERSION@.2">\n+<tool id="peptide_shaker" name="Peptide Shaker" version="@PEPTIDESHAKER_VERSION@.3">\n <description>\n Perform protein identification using various search engines based on results from SearchGUI\n </description>\n@@ -130,6 +130,11 @@\n \n 2>> $temp_stderr)\n \n+ ## If the user chose to zip the results but also export reports out of the zip, we have to unzip them\n+ #if $exporting_options.zip_conditional.zip_output_boolean == \'zip\' and $exporting_options.zip_conditional.export_reports_when_zip:\n+ && unzip \\$cwd/peptideshaker_output.zip \'reports/*\' -d \\$cwd/output_reports\n+ #end if\n+\n \t #if len(output_reports_list)>0:\n #if \'0\' in $output_reports_list:\n && find \\$cwd/output_reports -name \'*Certificate_of_Analysis.txt\' -exec bash -c \'mv "$0" "certificate.txt"\' {} \\;\n@@ -287,7 +292,9 @@\n <when value="separate">\n <param name="export_cps" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Exports the CPS file" />\n </when>\n- <when value="zip" />\n+ <when value="zip">\n+ <param name="export_reports_when_zip" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Also export reports out of the zip" />\n+ </when>\n </conditional>\n \n <param name="output_reports" type="select" display="checkboxes" multiple="True" optional="true" label="Reports to be generated">\n@@ -310,7 +317,7 @@\n </inputs>\n <outputs>\n <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">\n- <filter>exporting_options[\'zip_conditional\'][\'zip_output_boolean\'] is False and mzidentml_conditional[\'mzidentml_creation\'] is True</filter>\n+ <filter>exporting_options[\'zip_conditional\'][\'zip_output_boolean\'] is False and exporting_options[\'mzidentml_conditional\'][\'mzidentml_creation\'] is True</filter>\n </data>\n <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cpsx" label="${tool.name} on ${on_string}: CPS file">\n <filter>exporting_options[\'zip_conditional\'][\'zip_output_boolean\'] is False and exporting_options[\'zip_conditional\'][\'export_cps\'] is True</filter>\n@@ -324,44 +331,44 @@\n </data>\n -->\n \t <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters">\n- <filter>exporting_options[\'zip_conditional\'][\'zip_output_boolean\'] is False and str(exporting_options[\'output_reports\']) != \'None\' and \'0\' in exporting_options[\'output_reports\']</filter>\n+ <filter>(exporting_options[\'zip_conditional\'][\'zip_output_boolean\'] is False or (exporting_options[\'zip_conditional\'][\'zip_output_boolean\'] is True and exporting_options[\'zip_conditional\'][\'export_reports_when_zip\'] is True) ) and str(exporting_options[\'output_reports\']) != \'None\' and \'0\' in exporting_options[\'output_reports\']</filter>\n </data>\n <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">\n- <filter>exporting_options[\'zip_conditional\'][\'zip_output_boolean\'] is False and str(exporting_options[\'output_reports\']) != \'None\' and \'1\' in exporting_options[\'output_reports\']</filter>\n+ <filter>(exporting_options[\'zip_conditional\'][\'zip_output_boolean\'] is False or (exporting_options[\'zip_conditional\'][\'zip_output_boolean\'] is True and exporting_options[\'zip_conditional\'][\'export_reports_when_zip\'] is True) ) and str(exporting_options[\'output_reports\']) != \'None\' and \'1\' in exporting_options[\'output_reports\']</filter>\n </data>\n <data format="tabular" name="output_psm_phosphorylation" from'..b'g_options[\'zip_conditional\'][\'zip_output_boolean\'] is True and exporting_options[\'zip_conditional\'][\'export_reports_when_zip\'] is True) ) and str(exporting_options[\'output_reports\']) != \'None\' and \'7\' in exporting_options[\'output_reports\']</filter>\n </data>\n <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report">\n- <filter>exporting_options[\'zip_conditional\'][\'zip_output_boolean\'] is False and str(exporting_options[\'output_reports\']) != \'None\' and \'8\' in exporting_options[\'output_reports\']</filter>\n+ <filter>(exporting_options[\'zip_conditional\'][\'zip_output_boolean\'] is False or (exporting_options[\'zip_conditional\'][\'zip_output_boolean\'] is True and exporting_options[\'zip_conditional\'][\'export_reports_when_zip\'] is True) ) and str(exporting_options[\'output_reports\']) != \'None\' and \'8\' in exporting_options[\'output_reports\']</filter>\n </data>\n <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report">\n- <filter>exporting_options[\'zip_conditional\'][\'zip_output_boolean\'] is False and str(exporting_options[\'output_reports\']) != \'None\' and \'9\' in exporting_options[\'output_reports\']</filter>\n+ <filter>(exporting_options[\'zip_conditional\'][\'zip_output_boolean\'] is False or (exporting_options[\'zip_conditional\'][\'zip_output_boolean\'] is True and exporting_options[\'zip_conditional\'][\'export_reports_when_zip\'] is True) ) and str(exporting_options[\'output_reports\']) != \'None\' and \'9\' in exporting_options[\'output_reports\']</filter>\n </data>\n <data format="tabular" name="output_proteins_nonvalidated" from_work_dir="proteins_nonvalidated.txt" label="${tool.name} on ${on_string}: Protein Repor with non-validated matches">\n- <filter>exporting_options[\'zip_conditional\'][\'zip_output_boolean\'] is False and str(exporting_options[\'output_reports\']) != \'None\' and \'10\' in exporting_options[\'output_reports\']</filter>\n+ <filter>(exporting_options[\'zip_conditional\'][\'zip_output_boolean\'] is False or (exporting_options[\'zip_conditional\'][\'zip_output_boolean\'] is True and exporting_options[\'zip_conditional\'][\'export_reports_when_zip\'] is True) ) and str(exporting_options[\'output_reports\']) != \'None\' and \'10\' in exporting_options[\'output_reports\']</filter>\n </data>\n </outputs>\n <tests>\n- <test>\n+ <test expect_num_outputs="1">\n <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>\n <param name="processing_options_selector" value="no"/>\n <param name="filtering_options_selector" value="no"/>\n@@ -370,7 +377,7 @@\n <param name="export_cps" value="1"/>\n <output name="output_zip" file="peptide_shaker_modifications_result1.zip" ftype="zip" compare="sim_size" delta="3000" />\n </test>\n- <test>\n+ <test expect_num_outputs="12">\n <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>\n <param name="processing_options_selector" value="no"/>\n <param name="filtering_options_selector" value="yes"/>\n@@ -391,7 +398,7 @@\n <output name="output_proteins_phosphorylation" file="peptide_shaker_modifications_result1.output_proteins_phosphorylation" ftype="tabular"/>\n <output name="output_proteins_nonvalidated" file="peptide_shaker_modifications_result1.output_proteins_nonvalidated" ftype="tabular"/>\n </test>\n- <test>\n+ <test expect_num_outputs="2">\n <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>\n <param name="processing_options_selector" value="no"/>\n <param name="filtering_options_selector" value="no"/>\n' |