| Previous changeset 42:9e20c34298e3 (2018-01-23) Next changeset 44:f35bb9d0c93e (2018-03-20) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad |
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modified:
macros.xml searchgui.xml |
| b |
| diff -r 9e20c34298e3 -r 7963340ab569 macros.xml --- a/macros.xml Tue Jan 23 08:48:07 2018 -0500 +++ b/macros.xml Mon Mar 05 10:09:34 2018 -0500 |
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| @@ -2,7 +2,7 @@ <xml name="stdio"> <stdio> <exit_code range="1:" level="fatal" description="Job Failed" /> - <regex match="java.*Exception" level="fatal" description="Java Exception"/> + <regex match="java.*Exception" level="fatal" description="Java Exception"/> <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/> <regex match="CompomicsError" level="fatal" description="Compomics Error"/> </stdio> @@ -17,8 +17,8 @@ -max_charge $precursor_options.max_charge -fi $precursor_options.forward_ion -ri $precursor_options.reverse_ion - -min_isotope ${precursor_options.min_isotope} - -max_isotope ${precursor_options.max_isotope} + -min_isotope ${precursor_options.min_isotope} + -max_isotope ${precursor_options.max_isotope} #if $protein_digest_options.digestion.cleavage == 'default': ## -enzyme "Trysin" -mc $protein_digest_options.digestion.missed_cleavages @@ -30,7 +30,7 @@ #silent $enzymes.append(str($digest.enzyme)) #silent $missed_cleavages.append(str($digest.missed_cleavages)) ## #silent $specificities.append(str($digest.specificity)) - #end for + #end for -enzyme "#echo ','.join($enzymes)#" -mc "#echo ','.join($missed_cleavages)#" ## -specificity "#echo ','.join($specificities)#" @@ -41,7 +41,7 @@ #set $fixed_mods_str = $protein_modification_options.fixed_modifications or '' #set $variable_mods_str = $protein_modification_options.variable_modifications or '' #if $fixed_mods_str - -fixed_mods "$fixed_mods_str" + -fixed_mods "$fixed_mods_str" #end if #if $variable_mods_str -variable_mods "$variable_mods_str" @@ -79,7 +79,7 @@ <option value="Trypsin + CNBr">Trypsin + CNBr</option> <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option> <option value="Trypsin, no P rule">Trypsin, no P rule</option> - <option value="Whole Protein">Whole Protein</option> + <option value="Whole Protein">Whole Protein</option> <option value="Asp-N">Asp-N</option> <option value="Glu-C">Glu-C</option> <option value="Asp-N + Glu-C">Asp-N + Glu-C</option> @@ -129,7 +129,7 @@ <param name="fragment_tol_units" type="select" label="Fragment Tolerance Units" help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions"> <option value="1">Parts per million (ppm)</option> - <option value="0">Daltons</option> + <option value="0" selected="true">Daltons</option> </param> <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance" help="Provide error value for fragment ions, based on instrument used"/> @@ -157,7 +157,7 @@ <column name="value" index="0" /> </options> </param> - <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" + <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items"> <options from_file="searchgui_mods.loc"> <column name="name" index="0" /> |
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| diff -r 9e20c34298e3 -r 7963340ab569 searchgui.xml --- a/searchgui.xml Tue Jan 23 08:48:07 2018 -0500 +++ b/searchgui.xml Mon Mar 05 10:09:34 2018 -0500 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.2">\n+<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.3">\n <description>\n Perform protein identification using various search engines and prepare results for input to Peptide Shaker\n </description>\n@@ -75,12 +75,12 @@\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_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@@ -93,9 +93,9 @@\n -xtandem_refine_spec_synt ${advanced_options.xtandem.xtandem_refine.xtandem_refine_spec_synt}\n -xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_pot}\n -xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_evalue}\n- \n+\n #end if\n- #else \n+ #else\n -xtandem_output_spectra 1\n #end if\n \n@@ -105,37 +105,37 @@\n -omssa_scale_prec ${advanced_options.omssa.scale_precursor}\n -omssa_estimate_charge ${advanced_options.omssa.estimate_charge}\n -omssa_memory ${advanced_options.omssa.omssa_memory}\n- -omssa_neutron ${advanced_options.omssa.omssa_neutron} \n- -omssa_low_intensity "${advanced_options.omssa.omssa_low_intensity}" \n- -omssa_high_intensity ${advanced_options.omssa.omssa_high_intensity} \n- -omssa_intensity_incr ${advanced_options.omssa.omssa_intensity_incr} \n- -omssa_single_window_wd ${advanced_options.omssa.omssa_single_window_wd} \n- -omssa_double_window_wd ${advanced_options.omssa.omssa_double_window_wd} \n- -omssa_single_window_pk ${advanced_options.omssa.omssa_single_window_pk} \n- -omssa_double_window_pk ${advanced_options.omssa.omssa_double_window_pk} \n- -omssa_min_ann_int_pks ${advanced_options.omssa.omssa_min_ann_int_pks} \n- -omssa_min_annotated_peaks ${advanced_options.omssa.omssa_min_annotated_peaks} \n- -omssa_min_peaks ${advanced_options.omssa.omssa_min_peaks} \n- -omssa_methionine ${advanced_options.omssa.omssa_methionine} \n- -omssa_max_ladders ${advanced_options.omssa.omssa_max_ladders} \n- -omssa_max_frag_charge ${advanced_options.omssa.omssa_max_frag_charge} \n- -omssa_fraction ${advanced_options.omssa.omssa_fraction} \n- -omssa_plus_one ${advanced_options.omssa.omssa_plus_one} \n- -omssa_charge ${advanced_options.omssa.oms'..b'"integer" value="3"\n label="Comet: Maximum Fragment Charge" help="Sets the maximum fragment charge (fill value between 1 and 5)" />\n- <param name="comet_remove_meth" type="boolean" truevalue="1" falsevalue="0" checked="false" \n+ <param name="comet_remove_meth" type="boolean" truevalue="1" falsevalue="0" checked="false"\n label="Comet: Remove Methionine" help="Specifies whether the N-terminal methionine is cleaved prior to matching" />\n <param name="comet_batch_size" type="integer" value="0"\n label="Comet: Batch Size" help="0 means load and search all spectra at once, otherwise spectra are loaded and searched in batches of the number specified" />\n <param name="comet_num_ptms" type="integer" value="10"\n- label="Comet: Maximum Number of PTMs" help="The maximum number of ptms per peptide" /> \n+ label="Comet: Maximum Number of PTMs" help="The maximum number of ptms per peptide" />\n </when>\n </conditional>\n <!-- Fragment Ions Related parameters -->\n@@ -1011,10 +1023,8 @@\n <when value="yes">\n <param name="comet_frag_bin_offset" type="float" value="0.4"\n label="Comet: Fragment Bin Offset" help="Controls how each fragment bin is defined in terms of where each bin starts" />\n- <param name="comet_sparse_matrix" type="boolean" truevalue="1" falsevalue="0" checked="true" \n- label="Comet: Fragment Sparse Matrix" help="Controls whether or not internal sparse matrix data representation is used to lower memory usage" />\n <param name="comet_theoretical_fragment_ions" type="integer" value="0"\n- label="Comet: Theoretical Fragment Ions" help="Specifies how theoretical fragment ion peaks are represented (0 or 1 values are allowed)" /> \n+ label="Comet: Theoretical Fragment Ions" help="Specifies how theoretical fragment ion peaks are represented (0 or 1 values are allowed)" />\n </when>\n </conditional>\n </when>\n@@ -1052,7 +1062,7 @@\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+\n <conditional name="novor">\n <param name="novor_advanced" type="select" label="Novor Options">\n <option value="yes">Advanced</option>\n@@ -1090,7 +1100,7 @@\n <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>\n <param name="xtandem.xtandem_advanced" value="yes"/>\n <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>\n- <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> \n+ <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />\n </test>\n <!-- Test that search works with MSAmanda -->\n <test>\n@@ -1102,7 +1112,7 @@\n <param name="min_charge" value="1"/>\n <param name="max_charge" value="3"/>\n <param name="engines" value="MS_Amanda"/>\n- <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> \n+ <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />\n </test>\n </tests>\n <help>\n' |