comparison peptide_shaker.xml @ 38:79e37eff006d draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 48984afa5f3d1b80ecbbff2847645c15acd81fe6

37:7f2aeb19650f

<tool id="peptide_shaker" name="Peptide Shaker" version="1.16.3">
    <description>
        Perform protein identification using various search engines based on results from SearchGUI
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1.16.3">peptide-shaker</requirement>
    </requirements>
    <expand macro="stdio" />
    <command>
<![CDATA[
        #from datetime import datetime

                    -score_neutral_losses "${processing_options.ptm_score.neutral_losses}"
                    #if str($processing_options.ptm_score.ptm_threshold) != ''
                        -ptm_threshold "${processing_options.ptm_score.ptm_threshold}"
                    #end if
                #end if
                -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}"
                -ptm_alignment "${processing_options.ptm_alignment}"
            #end if

           ##Optional filtering parameters:
            #if $filtering_options.filtering_options_selector == "yes":
                -import_peptide_length_min "${filtering_options.min_peptide_length}"

                    help="default 95%: '95.0'" />
                <conditional name="ptm_score">
                    <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>
                    </param>
                    <when value="0" />
                    <when value="1">
                        <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
                        <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>
                </conditional>
                <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>
        </conditional>
        <conditional name="filtering_options">

38:79e37eff006d

<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>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1.16.4">peptide-shaker</requirement>
    </requirements>
    <expand macro="stdio" />
    <command>
<![CDATA[
        #from datetime import datetime

                    -score_neutral_losses "${processing_options.ptm_score.neutral_losses}"
                    #if str($processing_options.ptm_score.ptm_threshold) != ''
                        -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}"
            #end if

           ##Optional filtering parameters:
            #if $filtering_options.filtering_options_selector == "yes":
                -import_peptide_length_min "${filtering_options.min_peptide_length}"

                    help="default 95%: '95.0'" />
                <conditional name="ptm_score">
                    <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">
                        <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
                        <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>
        </conditional>
        <conditional name="filtering_options">