| Previous changeset 44:f35bb9d0c93e (2018-03-20) Next changeset 46:baeced706dbc (2018-07-11) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544 |
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modified:
macros.xml peptide_shaker.xml searchgui.xml |
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| diff -r f35bb9d0c93e -r 5fa8b409599e macros.xml --- a/macros.xml Tue Mar 20 05:09:36 2018 -0400 +++ b/macros.xml Mon Apr 30 04:41:50 2018 -0400 |
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| @@ -49,7 +49,7 @@ </token> <token name="@SEARCHGUI_MAJOR_VERSION@">3</token> - <token name="@SEARCHGUI_VERSION@">3.2.13</token> + <token name="@SEARCHGUI_VERSION@">3.2.24</token> <xml name="general_options"> <section name="protein_digest_options" expanded="false" title="Protein Digestion Options"> |
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| diff -r f35bb9d0c93e -r 5fa8b409599e peptide_shaker.xml --- a/peptide_shaker.xml Tue Mar 20 05:09:36 2018 -0400 +++ b/peptide_shaker.xml Mon Apr 30 04:41:50 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="peptide_shaker" name="Peptide Shaker" version="1.16.17"> +<tool id="peptide_shaker" name="Peptide Shaker" version="1.16.20"> <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="1.16.17">peptide-shaker</requirement> + <requirement type="package" version="1.16.20">peptide-shaker</requirement> </requirements> <expand macro="stdio" /> <command> |
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| diff -r f35bb9d0c93e -r 5fa8b409599e searchgui.xml --- a/searchgui.xml Tue Mar 20 05:09:36 2018 -0400 +++ b/searchgui.xml Mon Apr 30 04:41:50 2018 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.4">\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@@ -158,7 +158,6 @@\n -ms_amanda_mono ${advanced_options.ms_amanda.ms_amanda_mono}\n #end if\n \n- #* Not working in tests\n #if $advanced_options.myrimatch.myrimatch_advanced == "yes"\n -myrimatch_min_pep_length ${advanced_options.myrimatch.myrimatch_min_pep_length}\n -myrimatch_max_pep_length ${advanced_options.myrimatch.myrimatch_max_pep_length}\n@@ -176,7 +175,7 @@\n -myrimatch_num_batches ${advanced_options.myrimatch.myrimatch_num_batches}\n -myrimatch_max_peak ${advanced_options.myrimatch.myrimatch_max_peak}\n #end if\n- *#\n+\n \n #* Not working in tests\n #if $advanced_options.andromeda.andromeda_advanced == "yes"\n@@ -456,8 +455,6 @@\n <option value="OMSSA" selected="True">OMSSA</option>\n <option value="Comet">Comet</option>\n <option value="Tide">Tide</option>\n- <!-- Not working in tests\n- -->\n <option value="MyriMatch">MyriMatch</option>\n <option value="MS_Amanda">MS_Amanda</option>\n <!-- Windows only\n@@ -846,17 +843,8 @@\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_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@@ -866,7 +854,6 @@\n \n \n <!-- MyriMatch ADVANCED PARAMETERS -->\n- <!-- Not working in tests\n <conditional name="myrimatch">\n <param name="myrimatch_advanced" type="select" label="MyriMatch Options">\n <option value="yes">Advanced</option>\n@@ -874,44 +861,45 @@\n </param>\n <when value="no" />\n <when value="yes">\n- <param name="myrimatch_min_pep_length" type="integer" value="6"\n+ <param name="myrimatch_min_pep_length" type="integer" value="8"\n label="MyriMatch: Minimum Peptide Length" help="Minimum length for a peptide to be considered" />\n <param name="myrimatch_max_pep_length" type="integer" value="30"\n label="MyriMatch: Maximum Peptide Length" help="Maximum length for a peptide to be considered" />\n- <param name="myrimatch_min_prec_mass" type="float" value="0.0"\n- label="MyriMatch: Minimum Peptide Mass" help="Minimum 1+ mass of parent ion to be considered" />'..b' label="MyriMatch: Number of PTMs" help="Set the number of PTMS allowed per peptide" />\n+ label="MyriMatch: Max Variable PTMs per Peptide" help="Set the number of PTMS allowed per peptide" />\n <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)">\n <option value="CID" selected="True">CID</option>\n+ <option value="HCD" >HCD</option>\n <option value="ETD" >ETD</option>\n </param>\n- <param name="myrimatch_termini" label="MyriMatch: Number of Enzymatic Termini" type="select" help="Select the number of enzymatic termini">\n- <option value="0">non-tryptic</option>\n- <option value="1" >semi-tryptic</option>\n- <option value="2" selected="True" >fully-tryptic</option>\n+ <param name="myrimatch_termini" label="MyriMatch: Enzymatic Terminals" type="select" help="Select the number of enzymatic terminals">\n+ <option value="0">None required</option>\n+ <option value="1">At least one</option>\n+ <option value="2" selected="True" >Both</option>\n </param>\n <param name="myrimatch_plus_three" type="boolean" truevalue="1" falsevalue="0" checked="true"\n- label="MyriMatch: Smart Plus Three Option" help="Defines what algorithms are used to generate a set of theoretical fragment ions" />\n+ label="MyriMatch: Use Smart Plus Three Option" help="Defines what algorithms are used to generate a set of theoretical fragment ions" />\n <param name="myrimatch_xcorr" type="boolean" truevalue="1" falsevalue="0" checked="false"\n- label="MyriMatch: Xcorr Option" help="a Sequest-like cross correlation score can be calculated for the top ranking hits" />\n+ label="MyriMatch: Compute Xcorr" help="a Sequest-like cross correlation score can be calculated for the top ranking hits" />\n <param name="myrimatch_tic_cutoff" type="float" value="0.98"\n- label="MyriMatch: TIC cutoff percentage" help="Cumulative ion current of picked peaks divided by TIC >= this value for peaks to be retained" />\n+ label="MyriMatch: TIC cutoff percentage" help="Cumulative ion current of picked peaks divided by TIC >= this value for peaks to be retained (0.0 - 1.0)" />\n <param name="myrimatch_intensity_classes" type="integer" value="3"\n label="MyriMatch: Number of Intensity Classes" help="Experimental spectra have their peaks stratified into this number of intensity classed" />\n <param name="myrimatch_class_multiplier" type="integer" value="2"\n- label="MyriMatch: Class Multiplier" help="Has to do with previous option, this parameter controls the size of each class relative to the class above" />\n+ label="MyriMatch: Class Size Multiplier" help="Has to do with previous option, this parameter controls the size of each class relative to the class above" />\n <param name="myrimatch_num_batches" type="integer" value="50"\n label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" />\n <param name="myrimatch_max_peak" type="integer" value="100"\n label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" />\n </when>\n </conditional>\n- -->\n+\n \n <!-- Andromeda ADVANCED PARAMETERS -->\n <!-- Windows only\n' |