comparison mzsqlite_psm_align.xml @ 5:af5f22779a8e draft

planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit d65efea03eb2db8a43e64599a4f899ead1a252ba-dirty

4:a96b2754171c

        <requirement type="package">twobitreader</requirement>
        <requirement type="package">pysam</requirement>
        <requirement type="package">gffutils</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/mzsqlite_psm_align.py'  
            #if $ref.ref_source == 'cached':
                --twobit='$ref.ref_loc.fields.path'
            #elif $ref.ref_source == 'history':
                --twobit='$ref.ref_file'
            #end if
            #if $gffutilsdb:
                --gffutils_file '$gffutilsdb'
            #end if
            #if $readlignments:
                --reads_bam '$readlignments'
            #end if
            #if 'probed' in str($output_formats).split(','):
               --probed '$probed'
            #end if
            #if 'prosam' in str($output_formats).split(','):

            <option value="prosam">pro.sam</option>
            <option value="probed">pro.bed</option>
        </param>
    </inputs>
    <outputs>
        <data name="prosam" format="sam">
            <filter>'prosam' in output_formats</filter>
        </data>
        <data name="probam" format="pro.bam">
            <filter>'probam' in output_formats</filter>
        </data>
        <data name="probed" format="pro.bed">
            <filter>'probed' in output_formats</filter>
        </data>
    </outputs>
    <help><![CDATA[

5:af5f22779a8e

        <requirement type="package">twobitreader</requirement>
        <requirement type="package">pysam</requirement>
        <requirement type="package">gffutils</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if $readlignments:
            ln -s -f '${$readlignments}' 'input.bam' &&
            ln -s -f '${$readlignments.metadata.bam_index}' 'input.bam.bai' &&
        #end if
        python '$__tool_directory__/mzsqlite_psm_align.py'  
            #if $ref.ref_source == 'cached':
                --twobit='$ref.ref_loc.fields.path'
            #elif $ref.ref_source == 'history':
                --twobit='$ref.ref_file'
            #end if
            #if $gffutilsdb:
                --gffutils_file '$gffutilsdb'
            #end if
            #if $readlignments:
                --reads_bam 'input.bam'
            #end if
            #if 'probed' in str($output_formats).split(','):
               --probed '$probed'
            #end if
            #if 'prosam' in str($output_formats).split(','):

            <option value="prosam">pro.sam</option>
            <option value="probed">pro.bed</option>
        </param>
    </inputs>
    <outputs>
        <data name="prosam" format="sam" label="pro.SAM on ${on_string}">
            <filter>'prosam' in output_formats</filter>
        </data>
        <data name="probam" format="bam" label="pro.Bam on ${on_string}">
            <filter>'probam' in output_formats</filter>
        </data>
        <data name="probed" format="bed" label="pro.Bed on ${on_string}">
            <filter>'probed' in output_formats</filter>
        </data>
    </outputs>
    <help><![CDATA[