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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 48984afa5f3d1b80ecbbff2847645c15acd81fe6 |
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modified:
macros.xml peptide_shaker.xml searchgui.xml |
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| diff -r 7f2aeb19650f -r 79e37eff006d macros.xml --- a/macros.xml Thu Mar 23 18:47:12 2017 -0400 +++ b/macros.xml Wed May 24 21:35:25 2017 -0400 |
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| @@ -49,7 +49,7 @@ </token> <token name="@SEARCHGUI_MAJOR_VERSION@">3</token> - <token name="@SEARCHGUI_VERSION@">3.2.11</token> + <token name="@SEARCHGUI_VERSION@">3.2.13</token> <xml name="general_options"> <section name="protein_digest_options" expanded="false" title="Protein Digestion Options"> |
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| diff -r 7f2aeb19650f -r 79e37eff006d peptide_shaker.xml --- a/peptide_shaker.xml Thu Mar 23 18:47:12 2017 -0400 +++ b/peptide_shaker.xml Wed May 24 21:35:25 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="peptide_shaker" name="Peptide Shaker" version="1.16.3"> +<tool id="peptide_shaker" name="Peptide Shaker" version="1.16.4"> <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="1.16.3">peptide-shaker</requirement> + <requirement type="package" version="1.16.4">peptide-shaker</requirement> </requirements> <expand macro="stdio" /> <command> @@ -51,8 +51,9 @@ -ptm_threshold "${processing_options.ptm_score.ptm_threshold}" #end if #end if + -ptm_alignment "${processing_options.ptm_alignment}" + -ptm_sequence_matching_type "${processing_options.ptm_sequence_matching_type}" -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}" - -ptm_alignment "${processing_options.ptm_alignment}" #end if ##Optional filtering parameters: @@ -205,6 +206,7 @@ <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization"> <option value="0" selected="True">A-score</option> <option value="1">PhosphoRS</option> + <option value="2">None</option> </param> <when value="0" /> <when value="1"> @@ -212,7 +214,13 @@ <param name="ptm_threshold" label="The threshold to use for the PTM scores" optional="true" value="" type="float" help="Automatic mode will be used if not set" /> </when> + <when value="2" /> </conditional> + <param name="ptm_sequence_matching_type" type="select" label="The PTM to peptide sequence matching type"> + <option value="0">Character Sequence</option> + <option value="1" selected="true">Amino Acids</option> + <option value="2">Indistinguishable Amino Acids</option> + </param> <param name="ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" type="boolean" truevalue="1" falsevalue="0" checked="true"/> <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} --> </when> |
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| diff -r 7f2aeb19650f -r 79e37eff006d searchgui.xml --- a/searchgui.xml Thu Mar 23 18:47:12 2017 -0400 +++ b/searchgui.xml Wed May 24 21:35:25 2017 -0400 |
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| @@ -7,6 +7,7 @@ </macros> <requirements> <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement> + <requirement type="package">zip</requirement> </requirements> <expand macro="stdio" /> <command> |