Mercurial > repos > galaxyp > peptideshaker
changeset 26:3ef5a7dd1a36 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
| author | galaxyp |
|---|---|
| date | Tue, 10 May 2016 06:33:08 -0400 |
| parents | 0986f68fb410 |
| children | 70dade9fb8e3 |
| files | macros.xml peptide_shaker.xml searchgui.xml searchgui_mods.loc.sample tool_dependencies.xml |
| diffstat | 5 files changed, 53 insertions(+), 29 deletions(-) [+] |
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--- a/macros.xml Sun Feb 21 11:13:24 2016 -0500 +++ b/macros.xml Tue May 10 06:33:08 2016 -0400 @@ -26,7 +26,7 @@ -ri $reverse_ion </token> <token name="@SEARCHGUI_MAJOR_VERSION@">2</token> - <token name="@SEARCHGUI_VERSION@">2.1</token> + <token name="@SEARCHGUI_VERSION@">2.8</token> <xml name="general_options"> <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units" help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions"> @@ -41,8 +41,10 @@ help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used"> <option value="Trypsin">Trypsin</option> <option value="Arg-C">Arg-C</option> + <option value="Semi-Arg-C">Semi-Arg-C</option> <option value="CNBr">CNBr</option> <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option> + <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option> <option value="Formic Acid">Formic Acid</option> <option value="Lys-C">Lys-C</option> <option value="Lys-C, no P rule">Lys-C, no P rule</option>
--- a/peptide_shaker.xml Sun Feb 21 11:13:24 2016 -0500 +++ b/peptide_shaker.xml Tue May 10 06:33:08 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="peptide_shaker" name="Peptide Shaker" version="1.1.1"> +<tool id="peptide_shaker" name="Peptide Shaker" version="1.10.0"> <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="1.1">peptide_shaker</requirement> + <requirement type="package" version="1.10">peptide_shaker</requirement> </requirements> <expand macro="stdio" /> <command> @@ -47,9 +47,9 @@ ##Optional processing parameters: #if $processing_options.processing_options_selector == "yes" - -protein_FDR "${processing_options.protein_fdr}" - -peptide_FDR "${processing_options.peptide_fdr}" - -psm_FDR "${processing_options.psm_fdr}" + -protein_fdr "${processing_options.protein_fdr}" + -peptide_fdr "${processing_options.peptide_fdr}" + -psm_fdr "${processing_options.psm_fdr}" -ptm_score "${processing_options.ptm_score.ptm_score_selector}" #if $processing_options.ptm_score.ptm_score_selector == 1 -score_neutral_losses "${processing_options.ptm_score.neutral_losses}" @@ -62,10 +62,10 @@ ##Optional filtering parameters: #if $filtering_options.filtering_options_selector == "yes": - -min_peptide_length "${filtering_options.min_peptide_length}" - -max_peptide_length "${filtering_options.max_peptide_length}" - -max_precursor_error "${filtering_options.max_precursor_error}" - -max_precursor_error_type "${filtering_options.max_precursor_error_type}" + -import_peptide_length_min "${filtering_options.min_peptide_length}" + -import_peptide_length_max "${filtering_options.max_peptide_length}" + -import_precurosor_mz "${filtering_options.max_precursor_error}" + -import_precurosor_mz_ppm "${filtering_options.max_precursor_error_type}" ##-max_xtandem_e "${filtering_options.max_xtandem_e}" ##-max_omssa_e "${filtering_options.max_omssa_e}" ##-max_mascot_e "${filtering_options.max_mascot_e}" @@ -493,8 +493,8 @@ <param name="max_precursor_error" type="float" label="Maximum Precursor Error" value="10" help="Next option specifies units (Da or ppm)" /> <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select"> - <option value="0">ppm</option> - <option value="1">Daltons</option> + <option value="1">ppm</option> + <option value="0">Daltons</option> </param> <!--param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" /--> <!--param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" /-->
--- a/searchgui.xml Sun Feb 21 11:13:24 2016 -0500 +++ b/searchgui.xml Tue May 10 06:33:08 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1"> +<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.0"> <description> Perform protein identification using various search engines and prepare results for input to Peptide Shaker </description> @@ -56,6 +56,7 @@ @GENERAL_PARAMETERS@ -db input_database.fasta + $use_gene_mapping #if $xtandem.xtandem_advanced == "yes" @@ -85,6 +86,8 @@ -xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_evalue} #end if + #else + -xtandem_output_spectra 1 #end if #if $omssa.omssa_advanced == "yes" @@ -143,6 +146,7 @@ -msgf_isotope_high ${msgf.msgf_isotope_high} #end if + #* Not working in tests #if $ms_amanda.ms_amanda_advanced == "yes" -ms_amanda_decoy ${ms_amanda.ms_amanda_decoy} -ms_amanda_max_evalue ${ms_amanda.ms_amanda_max_evalue} @@ -150,7 +154,9 @@ -ms_amanda_max_rank ${ms_amanda.ms_amanda_max_rank} -ms_amanda_mono ${ms_amanda.ms_amanda_mono} #end if + *# + #* Not working in tests #if $myrimatch.myrimatch_advanced == "yes" -myrimatch_min_pep_length ${myrimatch.myrimatch_min_pep_length} -myrimatch_max_pep_length ${myrimatch.myrimatch_max_pep_length} @@ -170,8 +176,9 @@ -myrimatch_num_batches ${myrimatch.myrimatch_num_batches} -myrimatch_max_peak ${myrimatch.myrimatch_max_peak} #end if + *# - #* + #* Not working in tests #if $andromeda.andromeda_advanced == "yes" -andromeda_max_pep_mass ${andromeda.andromeda_max_pep_mass} -andromeda_max_comb ${andromeda.andromeda_max_comb} @@ -191,7 +198,8 @@ -andromeda_max_psms ${andromeda.andromeda_max_psms} #end if *# - + + #* Not working in tests #if $tide.tide_advanced == "yes" -tide_num_ptms ${tide.tide_num_ptms} -tide_num_ptms_per_type ${tide.tide_num_ptms_per_type} @@ -230,6 +238,7 @@ -tide_export_pin ${tide.tide_export_pin} -tide_remove_temp ${tide.tide_remove_temp} #end if + *# #if $comet.comet_advanced == "yes" @@ -293,7 +302,7 @@ ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created ## the tree is generated afterwards in PeptideShaker - -protein_index 0 + ## -protein_index 0 ##-makeblastdb_folder \$BLAST_ROOT_DIR @@ -360,9 +369,7 @@ && - (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr) - - && + (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr); exit_code_for_galaxy=\$?; cat $temp_stderr 2>&1; @@ -378,6 +385,10 @@ label="Create a concatenated target/decoy database before running PeptideShaker" help="Selecting this option will help PeptideShaker calculate FDR values" /> + <param name="use_gene_mapping" type="boolean" truevalue="-useGeneMapping 1" falsevalue="-useGeneMapping 0" checked="false" + label="gene mappings will be used and saved along with the project (UniProt databases only)" + help="This should only be enabled for UniProt databaases" /> + <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)" help="Select appropriate MGF dataset(s) from history" /> @@ -385,12 +396,16 @@ <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> - <option value="MyriMatch">MyriMatch</option> - <option value="MS_Amanda">MS_Amanda</option> + <!-- Not working in tests + <option value="MyriMatch">MyriMatch</option> + <option value="MS_Amanda">MS_Amanda</option> + --> <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> + --> <!-- Windows only <option value="Andromeda">Andromeda</option> --> @@ -461,7 +476,7 @@ <param name="xtandem_output_sequences" help="Controls output of sequence information" label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" /> <param name="xtandem_output_spectra" help="Controls output of spectrum information" - label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="false" /> + label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" /> <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="text" help="Path to a spectrum data file for use by skyline." --> <conditional name="xtandem_refine"><!-- -xtandem_refine --> @@ -642,6 +657,7 @@ </conditional> <!-- MS-AMANDA ADVANCED PARAMETERS --> + <!-- Not working in tests <conditional name="ms_amanda"> <param name="ms_amanda_advanced" type="select" label="MS Amanda Options"> <option value="yes">Advanced</option> @@ -660,9 +676,11 @@ label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" /> </when> </conditional> + --> <!-- TIDE ADVANCED PARAMETERS --> + <!-- Not working in tests <conditional name="tide"> <param name="tide_advanced" type="select" label="TIDE Options"> <option value="yes">Advanced</option> @@ -766,8 +784,10 @@ 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 <conditional name="myrimatch"> <param name="myrimatch_advanced" type="select" label="MyriMatch Options"> <option value="yes">Advanced</option> @@ -816,6 +836,7 @@ label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" /> </when> </conditional> + --> <!-- Andromeda ADVANCED PARAMETERS --> <!-- Windows only
--- a/searchgui_mods.loc.sample Sun Feb 21 11:13:24 2016 -0500 +++ b/searchgui_mods.loc.sample Tue May 10 06:33:08 2016 -0400 @@ -23,13 +23,13 @@ Didehydro of T Diiodination of Y Dimethylation of K -Dimethylation of K 2H(4) Dimethylation of K 2H(6) +Dimethylation of K 2H(6) 13C(2) Dimethylation of R +Dimethylation of peptide N-term +Dimethylation of peptide N-term 2H(4) Dimethylation of peptide N-term 2H(6) Dimethylation of peptide N-term 2H(6) 13C(2) -Dimethylation of peptide N-term K -Dimethylation of peptide N-term K 2H(4) Dioxidation of M Dioxidation of W Farnesylation of C @@ -63,6 +63,7 @@ ICPL6 of K ICPL6 of peptide N-term Isoleucine 13C(6) 15N(1) +Label of K 2H(4) Leucine 13C(6) 15N(1) Lipoyl of K Lysine 13C(6)
--- a/tool_dependencies.xml Sun Feb 21 11:13:24 2016 -0500 +++ b/tool_dependencies.xml Tue May 10 06:33:08 2016 -0400 @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> - <package name="searchgui" version="2.1"> - <repository changeset_revision="42249a2266ba" name="package_searchgui_2_1" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="searchgui" version="2.8"> + <repository changeset_revision="33a7c9c42472" name="package_searchgui_2_8" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="peptide_shaker" version="1.1"> - <repository changeset_revision="aa9c3d729470" name="package_peptideshaker_1_1" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="peptide_shaker" version="1.10"> + <repository changeset_revision="63441af662c0" name="package_peptideshaker_1_10" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>