comparison peptide_shaker.xml @ 44:f35bb9d0c93e draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb

43:7963340ab569

<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

            -replicate 1
            -identification_files \$cwd/searchgui_input.zip
            -id_params \$cwd/SEARCHGUI_IdentificationParameters.par
            -out \$cwd/peptideshaker_output.cpsx
            -zip \$cwd/peptideshaker_output.zip

            -threads "\${GALAXY_SLOTS:-12}"

            ##Optional processing parameters:
            #if $processing_options.processing_options_selector == "yes"

                    -contact_address "[e-mail]"
                    -organization_name "University of Minnesota"
                    -organization_email "[e-mail]"
                    -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
                #end if
            2>> $temp_stderr) 
            &&
        #end if

        ## Generate Reports if the user has selected one of the 8 additional reports
        ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker 
        ## and will not be passed to the command line
        #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ):

            (peptide-shaker eu.isas.peptideshaker.cmd.ReportCLI
                --exec_dir="\$cwd/${bin_dir}"

    </inputs>
    <outputs>
        <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
            <filter>'mzidentML' in outputs</filter>
        </data>
        <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cps" label="${tool.name} on ${on_string}: CPS file">
            <filter>'cps' in outputs</filter>
        </data>
        <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive">
            <filter>'zip' in outputs</filter>
        </data>

                </assert_contents>
            </output>
            <output name="output_proteins_phosphorylation">
                <assert_contents>
                    <has_text text="Phosphosite" />
                    <has_text text="cds.comp41779_c0_seq1" />
                </assert_contents>
            </output>
        </test>
    </tests>

44:f35bb9d0c93e

<tool id="peptide_shaker" name="Peptide Shaker" version="1.16.17">
    <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="1.16.17">peptide-shaker</requirement>
    </requirements>
    <expand macro="stdio" />
    <command>
<![CDATA[
        #from datetime import datetime

            -replicate 1
            -identification_files \$cwd/searchgui_input.zip
            -id_params \$cwd/SEARCHGUI_IdentificationParameters.par
            -out \$cwd/peptideshaker_output.cpsx
            -zip \$cwd/peptideshaker_output.zip
            #set $cleaned_list = str($outputs).split(',')
            #if 'cps' in $cleaned_list:
                #silent $cleaned_list.remove('cps')
            #end if
            #if 'mzidentML' in $cleaned_list:
                #silent $cleaned_list.remove('mzidentML')
            #end if
            #if 'zip' in $cleaned_list:
                #silent $cleaned_list.remove('zip')
            #end if
            #if len($cleaned_list) > 0
              ## Only numbers are left over. These corresponds to different reports.
              -reports #echo ','.join($cleaned_list)#
            #end if

            -threads "\${GALAXY_SLOTS:-12}"

            ##Optional processing parameters:
            #if $processing_options.processing_options_selector == "yes"

                    -contact_address "[e-mail]"
                    -organization_name "University of Minnesota"
                    -organization_email "[e-mail]"
                    -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
                #end if
            2>> $temp_stderr)
            &&
        #end if

        ## Generate Reports if the user has selected one of the 8 additional reports
        ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker
        ## and will not be passed to the command line
        #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ):

            (peptide-shaker eu.isas.peptideshaker.cmd.ReportCLI
                --exec_dir="\$cwd/${bin_dir}"

    </inputs>
    <outputs>
        <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
            <filter>'mzidentML' in outputs</filter>
        </data>
        <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cpsx" label="${tool.name} on ${on_string}: CPS file">
            <filter>'cps' in outputs</filter>
        </data>
        <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive">
            <filter>'zip' in outputs</filter>
        </data>

                </assert_contents>
            </output>
            <output name="output_proteins_phosphorylation">
                <assert_contents>
                    <has_text text="Phosphosite" />
                    <has_text text="cds.comp41779_c0_seq1" />
                </assert_contents>
            </output>
        </test>
        <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="3,cps"/>
            <output name="output_cps" file="peptide_shaker_result1.cpsx" ftype="peptideshaker_archive" compare="sim_size" delta="3000"/>
            <output name="output_psm">
                <assert_contents>
                    <has_text text="cds.comp41779_c0_seq1" />
                </assert_contents>
            </output>
        </test>
    </tests>