| Previous changeset 32:ff592231f118 (2017-01-25) Next changeset 34:0ebf3d3e4c90 (2017-02-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 |
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modified:
macros.xml peptide_shaker.xml searchgui.xml test-data/peptide_shaker_result1.zip test-data/tiny_searchgui_result1.zip test-data/tiny_searchgui_result_amandaonly.zip |
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| diff -r ff592231f118 -r bce45e9e6d70 macros.xml --- a/macros.xml Wed Jan 25 15:37:43 2017 -0500 +++ b/macros.xml Mon Feb 06 21:53:07 2017 -0500 |
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| b'@@ -8,109 +8,159 @@\n </stdio>\n </xml>\n <token name="@GENERAL_PARAMETERS@">\n- -frag_tol "${fragment_tol}"\n+ -frag_tol "${precursor_options.fragment_tol}"\n ### -frag_ppm\n- -prec_tol "${precursor_ion_tol}"\n- -prec_ppm "${precursor_ion_tol_units}"\n- ### -digestion\n- ### multiple enzymes?\n- -enzyme "${enzyme}"\n- ### -specificity\n- ### value per enzyme\n- -mc $missed_cleavages\n- #set $fixed_mods_str = $fixed_modifications or \'\'\n- #set $variable_mods_str = $variable_modifications or \'\'\n+ -prec_tol "${precursor_options.precursor_ion_tol}"\n+ -prec_ppm "${precursor_options.precursor_ion_tol_units}"\n+\n+ -min_charge $precursor_options.min_charge\n+ -max_charge $precursor_options.max_charge\n+ -fi $precursor_options.forward_ion\n+ -ri $precursor_options.reverse_ion\n+ -min_isotope ${precursor_options.min_isotope} \n+ -max_isotope ${precursor_options.max_isotope} \n+ #if $protein_digest_options.digestion.cleavage == \'default\':\n+ ## -enzyme "Trysin"\n+ -mc $protein_digest_options.digestion.missed_cleavages\n+ #elif $protein_digest_options.digestion.cleavage == \'0\' and len($protein_digest_options.digestion.digests) > 0:\n+ #set $enzymes = []\n+ #set $missed_cleavages = []\n+ ## #set $specificities = []\n+ #for $i, $digest in enumerate($protein_digest_options.digestion.digests):\n+ #silent $enzymes.append(str($digest.enzyme))\n+ #silent $missed_cleavages.append(str($digest.missed_cleavages))\n+ ## #silent $specificities.append(str($digest.specificity))\n+ #end for \n+ -enzyme "#echo \',\'.join($enzymes)#"\n+ -mc "#echo \',\'.join($missed_cleavages)#"\n+ ## -specificity "#echo \',\'.join($specificities)#"\n+ #else:\n+ -digestion $protein_digest_options.digestion.cleavage\n+ #end if\n+\n+ #set $fixed_mods_str = $protein_modification_options.fixed_modifications or \'\'\n+ #set $variable_mods_str = $protein_modification_options.variable_modifications or \'\'\n #if $fixed_mods_str\n -fixed_mods "$fixed_mods_str" \n #end if\n #if $variable_mods_str\n -variable_mods "$variable_mods_str"\n #end if\n- -min_charge $min_charge\n- -max_charge $max_charge\n- -fi $forward_ion\n- -ri $reverse_ion\n- -min_isotope ${min_isotope} \n- -max_isotope ${max_isotope} \n \n </token>\n <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>\n- <token name="@SEARCHGUI_VERSION@">3.1.4</token>\n+ <token name="@SEARCHGUI_VERSION@">3.2.5</token>\n <xml name="general_options">\n- <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"\n- help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">\n- <option value="1">Parts per million (ppm)</option>\n- <option value="2">Daltons</option>\n- </param>\n- <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance"\n- help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>\n- <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)"\n- help="Provide error value for fragment ions, based on instrument used"/>\n- <param name="enzyme" type="select" label="Enzyme"\n- help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">\n- <option value="Trypsin">Trypsin</opt'..b'>\n+ <!--\n+ <param name="specificity" type="select" label="Specificity">\n+ <option value="0" selected="true">Specific at both termini</option>\n+ <option value="1">Semi-Specific - one terminus</option>\n+ <option value="2">Specific at the N-terminus only</option>\n+ <option value="3">Specific at the C-terminus only</option>\n+ </param>\n+ -->\n+ </repeat>\n+ </when>\n+ <when value="1"/>\n+ <when value="2"/>\n+ </conditional>\n+ </section>\n+\n+ <section name="precursor_options" expanded="false" title="Precursor Options">\n+ <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"\n+ help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">\n+ <option value="1">Parts per million (ppm)</option>\n+ <option value="2">Daltons</option>\n+ </param>\n+ <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance"\n+ help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>\n+ <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)"\n+ help="Provide error value for fragment ions, based on instrument used"/>\n+ <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>\n+ <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>\n+ <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment">\n+ <option value="a">a</option>\n+ <option value="b" selected="true">b</option>\n+ <option value="c">c</option>\n+ </param>\n+ <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment">\n+ <option value="x">x</option>\n+ <option value="y" selected="true">y</option>\n+ <option value="z">z</option>\n+ </param>\n+ <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" />\n+ <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" />\n+ </section>\n+\n+ <section name="protein_modification_options" expanded="false" title="Protein Modification Options">\n+ <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true"\n+ help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">\n+ <options from_file="searchgui_mods.loc">\n+ <column name="name" index="0" />\n+ <column name="value" index="0" />\n+ </options>\n+ </param>\n+ <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" \n+ help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">\n+ <options from_file="searchgui_mods.loc">\n+ <column name="name" index="0" />\n+ <column name="value" index="0" />\n+ </options>\n+ </param>\n+ </section>\n+\n </xml>\n \n <xml name="citations">\n' |
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| diff -r ff592231f118 -r bce45e9e6d70 peptide_shaker.xml --- a/peptide_shaker.xml Wed Jan 25 15:37:43 2017 -0500 +++ b/peptide_shaker.xml Mon Feb 06 21:53:07 2017 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="peptide_shaker" name="Peptide Shaker" version="1.13.6"> +<tool id="peptide_shaker" name="Peptide Shaker" version="1.14.6"> <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="1.13.6">peptide-shaker</requirement> + <requirement type="package" version="1.14.6">peptide-shaker</requirement> </requirements> <expand macro="stdio" /> <command> @@ -82,7 +82,7 @@ (peptide-shaker eu.isas.peptideshaker.cmd.MzidCLI --exec_dir="\$cwd/${bin_dir}" -in \$cwd/peptideshaker_output.zip - -output_file output.mzid + -output_file \$cwd/output.mzid #if $contact_options.contact_options_selector == "yes": -contact_first_name "$contact_options.contact_first_name" -contact_last_name "$contact_options.contact_last_name" @@ -337,7 +337,7 @@ <param name="processing_options_selector" value="no"/> <param name="filtering_options_selector" value="no"/> <param name="outputs" value="zip,3"/> - <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="900" /> + <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="3000" /> <output name="output_psm"> <assert_contents> <has_text text="cds.comp41779_c0_seq1" /> @@ -358,7 +358,7 @@ </output> <output name="output_hierarchical"> <assert_contents> - <has_text_matching expression="1.1\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2" /> + <has_text_matching expression="1.1\tcds.comp" /> </assert_contents> </output> <output name="output_psm"> |
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| diff -r ff592231f118 -r bce45e9e6d70 searchgui.xml --- a/searchgui.xml Wed Jan 25 15:37:43 2017 -0500 +++ b/searchgui.xml Mon Feb 06 21:53:07 2017 -0500 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1">\n+<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.0">\n <description>\n Perform protein identification using various search engines and prepare results for input to Peptide Shaker\n </description>\n@@ -23,7 +23,7 @@\n export HOME=\\$cwd;\n \n ## echo the search engines to run\n- echo "$engines";\n+ echo "$search_engines_options.engines";\n echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}";\n \n ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present\n@@ -41,7 +41,7 @@\n ###########################################\n #### Creating decoy database ####\n ###########################################\n- #if $create_decoy:\n+ #if $protein_database_options.create_decoy:\n echo "Creating decoy database.";\n searchgui eu.isas.searchgui.cmd.FastaCLI --exec_dir="\\$cwd/${bin_dir}" -in input_database.fasta -decoy &&\n rm input_database.fasta &&\n@@ -59,256 +59,256 @@\n @GENERAL_PARAMETERS@\n \n -db input_database.fasta\n- #if $use_gene_mapping:\n- $use_gene_mapping\n- $update_gene_mapping\n+ #if $protein_database_options.use_gene_mapping:\n+ $protein_database_options.use_gene_mapping\n+ $protein_database_options.update_gene_mapping\n #end if\n \n- #if $xtandem.xtandem_advanced == "yes"\n+ #if $advanced_options.xtandem.xtandem_advanced == "yes"\n \n- -xtandem_npeaks ${xtandem.xtandem_npeaks}\n- -xtandem_min_peaks ${xtandem.xtandem_min_peaks}\n- -xtandem_min_frag_mz ${xtandem.xtandem_min_frag_mz}\n- -xtandem_min_prec_mass ${xtandem.xtandem_min_prec_mass}\n- -xtandem_noise_suppr ${xtandem.xtandem_noise_suppr}\n- -xtandem_dynamic_range ${xtandem.xtandem_dynamic_range}\n- -xtandem_quick_acetyl ${xtandem.xtandem_quick_acetyl} \n- -xtandem_quick_pyro ${xtandem.xtandem_quick_pyro} \n- -xtandem_stp_bias ${xtandem.xtandem_stp_bias} \n- -xtandem_evalue ${xtandem.xtandem_evalue} \n- -xtandem_output_proteins ${xtandem.xtandem_output_proteins} \n- -xtandem_output_sequences ${xtandem.xtandem_output_sequences} \n- -xtandem_output_spectra ${xtandem.xtandem_output_spectra}\n- ## -xtandem_skyline_path ${xtandem.xtandem_skyline_path}\n+ -xtandem_npeaks ${advanced_options.xtandem.xtandem_npeaks}\n+ -xtandem_min_peaks ${advanced_options.xtandem.xtandem_min_peaks}\n+ -xtandem_min_frag_mz ${advanced_options.xtandem.xtandem_min_frag_mz}\n+ -xtandem_min_prec_mass ${advanced_options.xtandem.xtandem_min_prec_mass}\n+ -xtandem_noise_suppr ${advanced_options.xtandem.xtandem_noise_suppr}\n+ -xtandem_dynamic_range ${advanced_options.xtandem.xtandem_dynamic_range}\n+ -xtandem_quick_acetyl ${advanced_options.xtandem.xtandem_quick_acetyl} \n+ -xtandem_quick_pyro ${advanced_options.xtandem.xtandem_quick_pyro} \n+ -xtandem_stp_bias ${advanced_options.xtandem.xtandem_stp_bias} \n+ -xtandem_evalue ${advanced_options.xtandem.xtandem_evalue} \n+ -xtandem_output_proteins ${advanced_options.xtandem.xtandem_output_proteins} \n+ -xtandem_output_sequences ${advanced_options.xtandem.xtandem_output_sequences} \n+ -xtandem_output_spectra ${advanced_options.xtandem.xtandem_output_spectra}\n+ ## -xtandem_skyline_path ${advanced_options.xtandem.xtandem_skyline_path}\n \n- #if $xtandem.xtandem_refine.xtandem_refine_selector == "yes"\n+ '..b'ype="integer" value="20" label="DirecTag maximum tag count, default is \'20\'."/>\n+ <param name="directag_intensity_weight" type="float" value="1.0" label="DirecTag intensity score weight, default is \'1.0\'."/>\n+ <param name="directag_fidelity_weight" type="float" value="1.0" label="DirecTag fidelity score weight, default is \'1.0\'."/>\n+ <param name="directag_complement_weight" type="float" value="1.0" label="DirecTag complement_score_weight, default is \'1.0\'."/>\n+ </when>\n+ </conditional>\n+ \n+ <conditional name="novor">\n+ <param name="novor_advanced" type="select" label="Novor Options">\n+ <option value="yes">Advanced</option>\n+ <option value="no" selected="True">Default</option>\n </param>\n- <param name="directag_isotope_tolerance" type="float" value="0.25" label="DirecTag isotope mz tolerance, default is \'0.25\'."/>\n- <param name="directag_complement_tolerance" type="float" value="0.5" label="DirecTag complement mz tolerance, default is \'0.5\'."/>\n- <param name="directag_tag_length" type="integer" value="3" label="DirecTag tag length, default is \'3\'."/>\n- <param name="directag_max_var_mods" type="integer" value="2" label="DirecTag maximum variable modifications per sequence, default is \'2\'."/>\n- <param name="directag_max_tag_count" type="integer" value="20" label="DirecTag maximum tag count, default is \'20\'."/>\n- <param name="directag_intensity_weight" type="float" value="1.0" label="DirecTag intensity score weight, default is \'1.0\'."/>\n- <param name="directag_fidelity_weight" type="float" value="1.0" label="DirecTag fidelity score weight, default is \'1.0\'."/>\n- <param name="directag_complement_weight" type="float" value="1.0" label="DirecTag complement_score_weight, default is \'1.0\'."/>\n- </when>\n- </conditional>\n-\n- <conditional name="novor">\n- <param name="novor_advanced" type="select" label="Novor Options">\n- <option value="yes">Advanced</option>\n- <option value="no" selected="True">Default</option>\n- </param>\n- <when value="no" />\n- <when value="yes">\n- <param name="novor_fragmentation" type="select" label="Novor fragmentation method">\n- <option value="HCD" selected="True">HCD</option>\n- <option value="CID">CID</option>\n- </param>\n- <param name="novor_mass_analyzer" label="Novor: mass analyzer" type="select" help="Identifier of the instrument to generate MS/MS spectra">\n- <option value="FT" selected="True">FT</option>\n- <option value="Trap" >Trap</option>\n- <option value="TOF" >TOF</option>\n- </param>\n- </when>\n- </conditional>\n-\n+ <when value="no" />\n+ <when value="yes">\n+ <param name="novor_fragmentation" type="select" label="Novor fragmentation method">\n+ <option value="HCD" selected="True">HCD</option>\n+ <option value="CID">CID</option>\n+ </param>\n+ <param name="novor_mass_analyzer" label="Novor: mass analyzer" type="select" help="Identifier of the instrument to generate MS/MS spectra">\n+ <option value="FT" selected="True">FT</option>\n+ <option value="Trap" >Trap</option>\n+ <option value="TOF" >TOF</option>\n+ </param>\n+ </when>\n+ </conditional>\n+ </section>\n </inputs>\n <outputs>\n <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />\n' |
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