comparison diamond_view.xml @ 8:54f751e413f4 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"

7:62c9df8382c2

<tool id="bg_diamond_view" name="Diamond" version="@VERSION@" profile="19.01">
    <description>generate formatted output from DAA files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
    ## need to link because diamont tries to open dataset_xxx.dat.daa
    ln -s '$daa' input.daa &&
    diamond
        view
        --daa input.daa
        @OUTPUT_ARGS@
        @HITFILTER_ARGS@
        $forwardonly
        --compress '0'

        </test>
        <test>
            <param name="daa" ftype="daa" value="diamond_results.daa" />
            <conditional name="output">
                <param name="outfmt" value="6"/>
                <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
            </conditional>
            <output name="blast_tabular" file="diamond_results.tabular"/>
        </test>
        <test>
            <param name="daa" ftype="daa" value="diamond_results.daa" />
            <conditional name="output">
                <param name="outfmt" value="101"/>

8:54f751e413f4

<tool id="bg_diamond_view" name="Diamond view" version="@VERSION@" profile="19.01">
    <description>generate formatted output from DAA files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command detect_errors="aggressive"><![CDATA[
    ## need to link because diamont tries to open dataset_xxx.dat.daa
    ln -s '$daa' input.daa &&
    diamond
        view
        --threads \${GALAXY_SLOTS:-1}
        --daa input.daa
        @OUTPUT_ARGS@
        @HITFILTER_ARGS@
        $forwardonly
        --compress '0'

        </test>
        <test>
            <param name="daa" ftype="daa" value="diamond_results.daa" />
            <conditional name="output">
                <param name="outfmt" value="6"/>
                <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,cigar,scovhsp"/>
            </conditional>
            <output name="blast_tabular" file="diamond_view_results.tabular"/>
        </test>
        <test>
            <param name="daa" ftype="daa" value="diamond_results.daa" />
            <conditional name="output">
                <param name="outfmt" value="101"/>