view fasta_cli.xml @ 0:8b99cb00e1c4 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty

<tool id="fasta_cli" name="FastaCLI" version="1.0">
    <description>
        Appends decoy sequences to FASTA files
    </description>
    <macros>
        <import>macros_basic.xml</import>
    </macros>
    <requirements>
	<requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
	<requirement type="package" version="3.0">zip</requirement>
    </requirements>
    <expand macro="stdio" />
    <command>
<![CDATA[

        ## #set $temp_stderr = "searchgui_stderr"
        #set $bin_dir = "bin"

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

        ## echo the search engines to run
        ##echo "$search_engines_options.engines";
        echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}";

        cp "${input_database}" input_database.fasta;

        ###########################################
        ####       Creating decoy database     ####
        ###########################################

        echo "Creating decoy database.";
        searchgui eu.isas.searchgui.cmd.FastaCLI --exec_dir="\$cwd/${bin_dir}" -in input_database.fasta -decoy &&
        rm input_database.fasta;
        echo "Decoy database:";
        echo "\$cwd/input_database_concatenated_target_decoy.fasta";

        exit_code_for_galaxy=\$?;
        ## cat $temp_stderr 2>&1;
        (exit \$exit_code_for_galaxy)
]]>
    </command>
    <inputs>
        <param format="fasta" name="input_database" type="data" label="Protein Database"
            help="Select FASTA database from history"/>
    </inputs>
    <outputs>
        <data name="input_database_concatenated_target_decoy" format="fasta" from_work_dir="input_database_concatenated_target_decoy.fasta" label="${tool.name}: FASTA file with decoys on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
            <output name="input_database_concatenated_target_decoy" file="searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" compare="sim_size" delta="1000" />
        </test>
    </tests>
    <help>
**What it does**

Appends decoy sequences to FASTA files.
    </help>
    <expand macro="citations" />
</tool>