comparison peptide_shaker.xml @ 33:bce45e9e6d70 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312

32:ff592231f118

<tool id="peptide_shaker" name="Peptide Shaker" version="1.13.6">
    <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="1.13.6">peptide-shaker</requirement>
    </requirements>
    <expand macro="stdio" />
    <command>
<![CDATA[
        #from datetime import datetime

        #if 'mzidentML' in str($outputs).split(','):
            echo "Generating mzIdentML";
            (peptide-shaker eu.isas.peptideshaker.cmd.MzidCLI
                --exec_dir="\$cwd/${bin_dir}"
                -in \$cwd/peptideshaker_output.zip
                -output_file output.mzid
                #if $contact_options.contact_options_selector == "yes":
                    -contact_first_name "$contact_options.contact_first_name"
                    -contact_last_name "$contact_options.contact_last_name"
                    -contact_email "$contact_options.contact_email"
                    -contact_address "$contact_options.contact_address"

        <test>
            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
            <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_psm">
                <assert_contents>
                    <has_text text="cds.comp41779_c0_seq1" />
                </assert_contents>
            </output>

                    <has_text text="Carbamidomethylation of C" />
                </assert_contents>
            </output>
            <output name="output_hierarchical">
                <assert_contents>
                    <has_text_matching expression="1.1\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2" />
                </assert_contents>
            </output>
            <output name="output_psm">
                <assert_contents>
                    <not_has_text text="Phosphosite" />

33:bce45e9e6d70

<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>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1.14.6">peptide-shaker</requirement>
    </requirements>
    <expand macro="stdio" />
    <command>
<![CDATA[
        #from datetime import datetime

        #if 'mzidentML' in str($outputs).split(','):
            echo "Generating mzIdentML";
            (peptide-shaker eu.isas.peptideshaker.cmd.MzidCLI
                --exec_dir="\$cwd/${bin_dir}"
                -in \$cwd/peptideshaker_output.zip
                -output_file \$cwd/output.mzid
                #if $contact_options.contact_options_selector == "yes":
                    -contact_first_name "$contact_options.contact_first_name"
                    -contact_last_name "$contact_options.contact_last_name"
                    -contact_email "$contact_options.contact_email"
                    -contact_address "$contact_options.contact_address"

        <test>
            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
            <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="3000" />
            <output name="output_psm">
                <assert_contents>
                    <has_text text="cds.comp41779_c0_seq1" />
                </assert_contents>
            </output>

                    <has_text text="Carbamidomethylation of C" />
                </assert_contents>
            </output>
            <output name="output_hierarchical">
                <assert_contents>
                    <has_text_matching expression="1.1\tcds.comp" />
                </assert_contents>
            </output>
            <output name="output_psm">
                <assert_contents>
                    <not_has_text text="Phosphosite" />