Mercurial > repos > galaxyp > peptideshaker
changeset 44:f35bb9d0c93e draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
| author | galaxyp |
|---|---|
| date | Tue, 20 Mar 2018 05:09:36 -0400 |
| parents | 7963340ab569 |
| children | 5fa8b409599e |
| files | peptide_shaker.xml searchgui.xml test-data/peptide_shaker_result1.cpsx |
| diffstat | 3 files changed, 73 insertions(+), 36 deletions(-) [+] |
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--- 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**
--- a/searchgui.xml Mon Mar 05 10:09:34 2018 -0500 +++ b/searchgui.xml Tue Mar 20 05:09:36 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.3"> +<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.4"> <description> Perform protein identification using various search engines and prepare results for input to Peptide Shaker </description> @@ -200,9 +200,10 @@ #end if *# - #* Not working in tests #if $advanced_options.tide.tide_advanced == "yes" - -tide_num_ptms ${advanced_options.tide.tide_num_ptms} + #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != '': + -tide_num_ptms ${advanced_options.tide.tide_max_spectrum_mz} + #end if -tide_num_ptms_per_type ${advanced_options.tide.tide_num_ptms_per_type} -tide_min_pep_length ${advanced_options.tide.tide_min_pep_length} -tide_max_pep_length ${advanced_options.tide.tide_max_pep_length} @@ -210,8 +211,6 @@ -tide_max_prec_mass ${advanced_options.tide.tide_max_prec_mass} -tide_decoy_format ${advanced_options.tide.tide_decoy_format} -tide_keep_terminals ${advanced_options.tide.tide_keep_terminals} - - -tide_output_folder ${advanced_options.tide.tide_output_folder} -tide_print_peptides ${advanced_options.tide.tide_print_peptides} -tide_verbosity ${advanced_options.tide.tide_verbosity} -tide_monoisotopic ${advanced_options.tide.tide_monoisotopic} @@ -221,7 +220,9 @@ -tide_max_psms ${advanced_options.tide.tide_max_psms} -tide_compute_p ${advanced_options.tide.tide_compute_p} -tide_min_spectrum_mz ${advanced_options.tide.tide_min_spectrum_mz} - -tide_max_spectrum_mz ${advanced_options.tide.tide_max_spectrum_mz} + #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != '': + -tide_max_spectrum_mz ${advanced_options.tide.tide_max_spectrum_mz} + #end if -tide_min_spectrum_peaks ${advanced_options.tide.tide_min_spectrum_peaks} -tide_spectrum_charges ${advanced_options.tide.tide_spectrum_charges} -tide_remove_prec ${advanced_options.tide.tide_remove_prec} @@ -232,14 +233,21 @@ -tide_mz_bin_width ${advanced_options.tide.tide_mz_bin_width} -tide_mz_bin_offset ${advanced_options.tide.tide_mz_bin_offset} -tide_concat ${advanced_options.tide.tide_concat} - -tide_export_text ${advanced_options.tide.tide_export_text} - -tide_export_sqt ${advanced_options.tide.tide_export_sqt} - -tide_export_pepxml ${advanced_options.tide.tide_export_pepxml} - -tide_export_mzid ${advanced_options.tide.tide_export_mzid} - -tide_export_pin ${advanced_options.tide.tide_export_pin} + + #set $formats = ["tide_export_text", "tide_export_sqt", "tide_export_pepxml", "tide_export_mzid", "tide_export_pin"] + #for $format in $formats: + #if str($advanced_options.tide.tide_export).strip() == $format: + -$format 1 + #else: + -$format 0 + #end if + + #end for + -tide_remove_temp ${advanced_options.tide.tide_remove_temp} + #end if - *# + #if $advanced_options.comet.comet_advanced == "yes" @@ -439,7 +447,7 @@ help="Select appropriate MGF dataset(s) from history" /> <!-- Search Engine Selection --> - <section name="search_engines_options" expanded="false" title="Search Engine Options"> + <section name="search_engines_options" expanded="true" title="Search Engine Options"> <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines"> <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help> <option value="X!Tandem" selected="True">X!Tandem</option> @@ -447,8 +455,6 @@ <option value="MSGF" selected="True">MS-GF+</option> <option value="OMSSA" selected="True">OMSSA</option> <option value="Comet">Comet</option> - <!-- Not working in tests - --> <option value="Tide">Tide</option> <!-- Not working in tests --> @@ -748,7 +754,6 @@ <!-- TIDE ADVANCED PARAMETERS --> - <!-- Not working in tests <conditional name="tide"> <param name="tide_advanced" type="select" label="TIDE Options"> <option value="yes">Advanced</option> @@ -756,7 +761,7 @@ </param> <when value="no" /> <when value="yes"> - <param name="tide_num_ptms" type="integer" value="100" + <param name="tide_num_ptms" type="integer" value="" optional="true" label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/> <param name="tide_num_ptms_per_type" type="integer" value="2" label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/> @@ -782,8 +787,6 @@ </param> <param name="tide_decoy_seed" type="integer" value="1" label="TIDE: Decoy Seed" help="Set the decoy seed"/> - <param name="tide_output_folder" type="text" value="crux-output" - label="TIDE: Output Folder" help="Set the results output folder (relative to the Tide working folder)"/> <param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false" label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/> <param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress"> @@ -812,7 +815,7 @@ label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/> <param name="tide_min_spectrum_mz" type="float" value="0.0" label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/> - <param name="tide_max_spectrum_mz" type="float" value="100000.0" + <param name="tide_max_spectrum_mz" type="float" value="" optional="true" label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/> <param name="tide_min_spectrum_peaks" type="integer" value="20" label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/> @@ -838,21 +841,29 @@ label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/> <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false" label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/> - <param name="tide_export_text" type="boolean" truevalue="1" falsevalue="0" checked="true" - label="TIDE: Export Text" help="If true, a text-formatted output file is exported"/> - <param name="tide_export_sqt" type="boolean" truevalue="1" falsevalue="0" checked="false" - label="TIDE: Export SQT" help="If true, a sqt-formatted output file is exported"/> - <param name="tide_export_pepxml" type="boolean" truevalue="1" falsevalue="0" checked="false" - label="TIDE: Export Pepxml" help="If true, a pepxml output file is exported"/> - <param name="tide_export_mzid" type="boolean" truevalue="1" falsevalue="0" checked="false" - label="TIDE: Export Mzid" help="If true, a mzid output file is exported"/> - <param name="tide_export_pin" type="boolean" truevalue="1" falsevalue="0" checked="false" - label="TIDE: Export Percolator Input File" help="If true, a percolator input file is exported"/> + + <param name="tide_export" label="TIDE: Output Format" type="select" help="Choose the output format"> + <option value="tide_export_text" selected="True">Text</option> + <option value="tide_export_sqt" >SQT</option> + <option value="tide_export_pepxml" >pepxml</option> + <!-- + MZidentML and Percolator input file options generates files with the format (ie. if we use a spectrum file called ´qExactive01819´): + galaxy/database/jobs_directory/000/88/working/bin/resources/Tide/linux/linux_64bit/crux-output/qExactive01819.tide-search.target.mzid + instead of + galaxy/database/jobs_directory/000/88/working/bin/resources/Tide/linux/linux_64bit/crux-output/qExactive01819.tide-search.mzid + which is the expected one, so current searchgui version gives a "does not exist error". + --> + <!-- + <option value="tide_export_mzid" >MzIdentML</option + <option value="tide_export_pin" >Percolator input file</option> + --> + </param> + <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true" label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/> </when> </conditional> - --> + <!-- MyriMatch ADVANCED PARAMETERS --> <!-- Not working in tests