comparison ident_params.xml @ 57:da885ca16cb2 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"

56:1beff3ddce58

<tool id="ident_params" name="Identification Parameters" version="1.5.1">
    <description>
        Sets the identification parameters to be used in SearchGUI and PeptideShaker apps
    </description>
    <macros>
        <import>macros_basic.xml</import>

      	<requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
    </requirements>
    <expand macro="stdio" />
    <command>
<![CDATA[
        #set $temp_stderr = "searchgui_stderr"
        #set $bin_dir = "bin"

        mkdir output;
        cwd=`pwd`;
        export HOME=\$cwd;


        echo "" > $temp_stderr &&

        echo 'running Identification Parameters CLI' &&
        #####################################################
        ## generate IdentificationParameters for SearchGUI ##
        #####################################################
        (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI
            --exec_dir="./bin/"
            -out './IdentificationParametersOutput.par'

            ## SPECTRUM MATCHING PARAMETERS

                -fasta_decoy_tag $advanced_options.database_processing_options.decoy_conditional.decoy_tag
                -fasta_decoy_type $advanced_options.database_processing_options.decoy_conditional.decoy_type
            #end if
                -fasta_target_decoy 0
                -fasta_decoy_file_tag $advanced_options.database_processing_options.decoy_file_tag

        2> $temp_stderr) &&

        cat $temp_stderr 2>&1;
]]>
    </command>
    <inputs>

57:da885ca16cb2

<tool id="ident_params"
      name="Identification Parameters"
      version="1.5.1"
      profile="20.01"
>
    <description>
        Sets the identification parameters to be used in SearchGUI and PeptideShaker apps
    </description>
    <macros>
        <import>macros_basic.xml</import>

      	<requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
    </requirements>
    <expand macro="stdio" />
    <command>
<![CDATA[
        #set $bin_dir = "bin"

        mkdir output;
        cwd=`pwd`;
        export HOME=\$cwd;



        echo 'running Identification Parameters CLI' &&
        #####################################################
        ## generate IdentificationParameters for SearchGUI ##
        #####################################################
        searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI
            --exec_dir="./bin/"
            -out './IdentificationParametersOutput.par'

            ## SPECTRUM MATCHING PARAMETERS

                -fasta_decoy_tag $advanced_options.database_processing_options.decoy_conditional.decoy_tag
                -fasta_decoy_type $advanced_options.database_processing_options.decoy_conditional.decoy_type
            #end if
                -fasta_target_decoy 0
                -fasta_decoy_file_tag $advanced_options.database_processing_options.decoy_file_tag
]]>
    </command>
    <inputs>