| Previous changeset 43:7963340ab569 (2018-03-05) Next changeset 45:5fa8b409599e (2018-04-30) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb |
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modified:
peptide_shaker.xml searchgui.xml |
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added:
test-data/peptide_shaker_result1.cpsx |
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| diff -r 7963340ab569 -r f35bb9d0c93e peptide_shaker.xml --- a/peptide_shaker.xml Mon Mar 05 10:09:34 2018 -0500 +++ b/peptide_shaker.xml Tue Mar 20 05:09:36 2018 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="peptide_shaker" name="Peptide Shaker" version="1.16.4"> +<tool id="peptide_shaker" name="Peptide Shaker" version="1.16.17"> <description> Perform protein identification using various search engines based on results from SearchGUI </description> @@ -6,7 +6,7 @@ <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="1.16.4">peptide-shaker</requirement> + <requirement type="package" version="1.16.17">peptide-shaker</requirement> </requirements> <expand macro="stdio" /> <command> @@ -36,6 +36,20 @@ -id_params \$cwd/SEARCHGUI_IdentificationParameters.par -out \$cwd/peptideshaker_output.cpsx -zip \$cwd/peptideshaker_output.zip + #set $cleaned_list = str($outputs).split(',') + #if 'cps' in $cleaned_list: + #silent $cleaned_list.remove('cps') + #end if + #if 'mzidentML' in $cleaned_list: + #silent $cleaned_list.remove('mzidentML') + #end if + #if 'zip' in $cleaned_list: + #silent $cleaned_list.remove('zip') + #end if + #if len($cleaned_list) > 0 + ## Only numbers are left over. These corresponds to different reports. + -reports #echo ','.join($cleaned_list)# + #end if -threads "\${GALAXY_SLOTS:-12}" @@ -107,12 +121,12 @@ -organization_email "galaxyp@umn.edu" -organization_address "Minneapolis, MN 55455, Vereinigte Staaten" #end if - 2>> $temp_stderr) + 2>> $temp_stderr) && #end if ## Generate Reports if the user has selected one of the 8 additional reports - ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker + ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker ## and will not be passed to the command line #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ): @@ -305,7 +319,7 @@ <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file"> <filter>'mzidentML' in outputs</filter> </data> - <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cps" label="${tool.name} on ${on_string}: CPS file"> + <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cpsx" label="${tool.name} on ${on_string}: CPS file"> <filter>'cps' in outputs</filter> </data> <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive"> @@ -406,6 +420,18 @@ </assert_contents> </output> </test> + <test> + <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> + <param name="processing_options_selector" value="no"/> + <param name="filtering_options_selector" value="no"/> + <param name="outputs" value="3,cps"/> + <output name="output_cps" file="peptide_shaker_result1.cpsx" ftype="peptideshaker_archive" compare="sim_size" delta="3000"/> + <output name="output_psm"> + <assert_contents> + <has_text text="cds.comp41779_c0_seq1" /> + </assert_contents> + </output> + </test> </tests> <help> **What it does** |
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| diff -r 7963340ab569 -r f35bb9d0c93e searchgui.xml --- a/searchgui.xml Mon Mar 05 10:09:34 2018 -0500 +++ b/searchgui.xml Tue Mar 20 05:09:36 2018 -0400 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.3">\n+<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.4">\n <description>\n Perform protein identification using various search engines and prepare results for input to Peptide Shaker\n </description>\n@@ -200,9 +200,10 @@\n #end if\n *#\n \n- #* Not working in tests\n #if $advanced_options.tide.tide_advanced == "yes"\n- -tide_num_ptms ${advanced_options.tide.tide_num_ptms}\n+ #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != \'\':\n+ -tide_num_ptms ${advanced_options.tide.tide_max_spectrum_mz}\n+ #end if\n -tide_num_ptms_per_type ${advanced_options.tide.tide_num_ptms_per_type}\n -tide_min_pep_length ${advanced_options.tide.tide_min_pep_length}\n -tide_max_pep_length ${advanced_options.tide.tide_max_pep_length}\n@@ -210,8 +211,6 @@\n -tide_max_prec_mass ${advanced_options.tide.tide_max_prec_mass}\n -tide_decoy_format ${advanced_options.tide.tide_decoy_format}\n -tide_keep_terminals ${advanced_options.tide.tide_keep_terminals}\n-\n- -tide_output_folder ${advanced_options.tide.tide_output_folder}\n -tide_print_peptides ${advanced_options.tide.tide_print_peptides}\n -tide_verbosity ${advanced_options.tide.tide_verbosity}\n -tide_monoisotopic ${advanced_options.tide.tide_monoisotopic}\n@@ -221,7 +220,9 @@\n -tide_max_psms ${advanced_options.tide.tide_max_psms}\n -tide_compute_p ${advanced_options.tide.tide_compute_p}\n -tide_min_spectrum_mz ${advanced_options.tide.tide_min_spectrum_mz}\n- -tide_max_spectrum_mz ${advanced_options.tide.tide_max_spectrum_mz}\n+ #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != \'\':\n+ -tide_max_spectrum_mz ${advanced_options.tide.tide_max_spectrum_mz}\n+ #end if\n -tide_min_spectrum_peaks ${advanced_options.tide.tide_min_spectrum_peaks}\n -tide_spectrum_charges ${advanced_options.tide.tide_spectrum_charges}\n -tide_remove_prec ${advanced_options.tide.tide_remove_prec}\n@@ -232,14 +233,21 @@\n -tide_mz_bin_width ${advanced_options.tide.tide_mz_bin_width}\n -tide_mz_bin_offset ${advanced_options.tide.tide_mz_bin_offset}\n -tide_concat ${advanced_options.tide.tide_concat}\n- -tide_export_text ${advanced_options.tide.tide_export_text}\n- -tide_export_sqt ${advanced_options.tide.tide_export_sqt}\n- -tide_export_pepxml ${advanced_options.tide.tide_export_pepxml}\n- -tide_export_mzid ${advanced_options.tide.tide_export_mzid}\n- -tide_export_pin ${advanced_options.tide.tide_export_pin}\n+\n+ #set $formats = ["tide_export_text", "tide_export_sqt", "tide_export_pepxml", "tide_export_mzid", "tide_export_pin"]\n+ #for $format in $formats:\n+ #if str($advanced_options.tide.tide_export).strip() == $format:\n+ -$format 1\n+ #else:\n+ -$format 0\n+ #end if\n+\n+ #end for\n+\n -tide_remove_temp ${advanced_options.tide.tide_remove_temp}\n+\n #end if\n- *#\n+\n \n #if $advanced_options.comet.comet_advanced == "yes"\n \n@@ -439,7 +447,7 @@\n help="Select appropriate MGF dataset(s) from history" />\n \n <!-- Search Engine Selection -->\n- <section name="search_engines_options" expanded="false" title="Search Engine Options">\n+ <section name="search_engines_options" expanded="true" title="Search Engine Options">\n <param name="engines" type="select" display="checkboxes" m'..b'label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/>\n <param name="tide_min_spectrum_mz" type="float" value="0.0"\n label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/>\n- <param name="tide_max_spectrum_mz" type="float" value="100000.0"\n+ <param name="tide_max_spectrum_mz" type="float" value="" optional="true"\n label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/>\n <param name="tide_min_spectrum_peaks" type="integer" value="20"\n label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/>\n@@ -838,21 +841,29 @@\n label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/>\n <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false"\n label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/>\n- <param name="tide_export_text" type="boolean" truevalue="1" falsevalue="0" checked="true"\n- label="TIDE: Export Text" help="If true, a text-formatted output file is exported"/>\n- <param name="tide_export_sqt" type="boolean" truevalue="1" falsevalue="0" checked="false"\n- label="TIDE: Export SQT" help="If true, a sqt-formatted output file is exported"/>\n- <param name="tide_export_pepxml" type="boolean" truevalue="1" falsevalue="0" checked="false"\n- label="TIDE: Export Pepxml" help="If true, a pepxml output file is exported"/>\n- <param name="tide_export_mzid" type="boolean" truevalue="1" falsevalue="0" checked="false"\n- label="TIDE: Export Mzid" help="If true, a mzid output file is exported"/>\n- <param name="tide_export_pin" type="boolean" truevalue="1" falsevalue="0" checked="false"\n- label="TIDE: Export Percolator Input File" help="If true, a percolator input file is exported"/>\n+\n+ <param name="tide_export" label="TIDE: Output Format" type="select" help="Choose the output format">\n+ <option value="tide_export_text" selected="True">Text</option>\n+ <option value="tide_export_sqt" >SQT</option>\n+ <option value="tide_export_pepxml" >pepxml</option>\n+ <!--\n+ MZidentML and Percolator input file options generates files with the format (ie. if we use a spectrum file called \xc2\xb4qExactive01819\xc2\xb4):\n+ galaxy/database/jobs_directory/000/88/working/bin/resources/Tide/linux/linux_64bit/crux-output/qExactive01819.tide-search.target.mzid\n+ instead of\n+ galaxy/database/jobs_directory/000/88/working/bin/resources/Tide/linux/linux_64bit/crux-output/qExactive01819.tide-search.mzid\n+ which is the expected one, so current searchgui version gives a "does not exist error".\n+ -->\n+ <!--\n+ <option value="tide_export_mzid" >MzIdentML</option\n+ <option value="tide_export_pin" >Percolator input file</option>\n+ -->\n+ </param>\n+\n <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true"\n label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/>\n </when>\n </conditional>\n- -->\n+\n \n <!-- MyriMatch ADVANCED PARAMETERS -->\n <!-- Not working in tests\n' |
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| diff -r 7963340ab569 -r f35bb9d0c93e test-data/peptide_shaker_result1.cpsx |
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| Binary file test-data/peptide_shaker_result1.cpsx has changed |