comparison probamconvert.xml @ 1:37369e255465 draft default tip

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0:0a77e0c00146

    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        #set $psm_file = input.${input.datatype.file_ext}
        ln -s "$input" $psm_file;
        proBAM.py --name="converted" --file=$psm_file 
        --database=$refsrc.database
        #if str($refsrc.database) == 'ENSEMBL':
            --species=$refsrc.species
            #if $refsrc.version:
                --version=$refsrc.version
            #end if
        #end if
        #if str($optional.decoy_annotation) != 'None':
            --decoy_annotation='$optional.decoy_annotation'
        #end if
        --pre_picked_annotation=$pre_picked_annotation
        --mismatches=$optional.mismatches
        $optional.rm_duplicates
        $optional.three_frame_translation
        $optional.include_unmapped
        --directory=outputs
    ]]></command>
    <inputs>
        <param name="input" type="data" format="mzid,pepxml" label="Peptide Indentification (mzIdentML or pepXML)"/>
        <param name="conversion_mode" type="select" label="Convert to:">
            <option value="proBAM_psm">proBAM_psm</option>

                <option value="First">First</option>
            </param>
         </section>
    </inputs>
    <outputs>
        <data name="output_bam" format="pro.bam" label="" from_work_dir="outputs/converted.sorted.bam">
            <filter>conversion_mode != 'proBED'</filter>
        </data>
        <data name="output_bed" format="pro.bed" label="" from_work_dir="outputs/converted.pro.bed">
            <filter>conversion_mode == 'proBED'</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" ftype="mzid" value="test.mzid"/>
            <param name="conversion_mode" value="proBAM_psm"/>
            <param name="database" value="ENSEMBL"/>
            <param name="species" value="homo_sapiens"/>
            <param name="version" value="87"/>
            <output name="output_bam">
                <assert_contents>
                    <has_text text="Q7Z6Z7_0" />
                </assert_contents>
            </output>
        </test>

1:37369e255465

    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        #set $psm_file = 'input.'+str($input.datatype.file_ext)
        ln -s "$input" $psm_file;
        proBAM.py --name="converted" --file=$psm_file --conversion_mode=$conversion_mode
        --database=$refsrc.database
        #if str($refsrc.database) == 'ENSEMBL':
            --species=$refsrc.species
            #if $refsrc.version:
                --version=$refsrc.version
            #end if
        #end if
        #if str($optional.decoy_annotation) != '':
            --decoy_annotation='$optional.decoy_annotation'
        #end if
        --pre_picked_annotation=$optional.pre_picked_annotation
        --mismatches=$optional.mismatches
        $optional.rm_duplicates
        $optional.three_frame_translation
        $optional.include_unmapped
    ]]></command>
    <inputs>
        <param name="input" type="data" format="mzid,pepxml" label="Peptide Indentification (mzIdentML or pepXML)"/>
        <param name="conversion_mode" type="select" label="Convert to:">
            <option value="proBAM_psm">proBAM_psm</option>

                <option value="First">First</option>
            </param>
         </section>
    </inputs>
    <outputs>
        <data name="output_bam" format="bam" label="${conversion_mode} ${input.display_name}.pro.bam" from_work_dir="converted.sorted.bam">
            <filter>conversion_mode != 'proBED'</filter>
        </data>
        <data name="output_bed" format="bed" label="${conversion_mode} ${input.display_name}.pro.bed" from_work_dir="converted.pro.bed">
            <filter>conversion_mode == 'proBED'</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" ftype="mzid" value="test.mzid"/>
            <param name="conversion_mode" value="proBED"/>
            <param name="database" value="ENSEMBL"/>
            <param name="species" value="homo_sapiens"/>
            <param name="version" value="87"/>
            <output name="output_bed">
                <assert_contents>
                    <has_text text="Q7Z6Z7_0" />
                </assert_contents>
            </output>
        </test>