comparison mitokmer.xml @ 3:c9d98f5bc240 draft

planemo upload commit 003cdb83fd17248ef57959332d58a3c96311332a-dirty

2:a0852bb4b09b

        #set $rev = "none"
        #end if
        python $__tool_directory__/kmer_read_m3.py
        -w $__tool_directory__
        -d $__tool_directory__/output
        -i $__tool_directory__/$fwd $__tool_directory__/$rev
    ]]></command>
    <inputs>

        <conditional name="reads">
            <param name="reads_select" type="select" label="One FASTQ dataset from your history, or two datasets from your history">

            </when>
        </conditional>

    </inputs>
    <outputs>
      <data format="tabular" label="mitokmer Results" name="results" from_work_dir="output/mitokmer_result.csv"/>
    </outputs>
    <tests>
        <test>
         <param name="reads_select" value="single" />
         <param name="allreads" value="1a.fasta" format="fasta"/>
         <output name="output1" file="mitokmer_result.csv"/>
        </test>
    </tests>

    <help><![CDATA[

3:c9d98f5bc240

        #set $rev = "none"
        #end if
        python $__tool_directory__/kmer_read_m3.py
        -w $__tool_directory__
        -d $__tool_directory__/output
        -i $__tool_directory__/$fwd $__tool_directory__/$rev;
        echo "run cat";
        rm $__tool_directory__/results*;
        cat $__tool_directory__/output/mitokmer_result.csv > $__tool_directory__/results.csv;
    ]]></command>
    <inputs>

        <conditional name="reads">
            <param name="reads_select" type="select" label="One FASTQ dataset from your history, or two datasets from your history">

            </when>
        </conditional>

    </inputs>
    <outputs>
      <data format="tabular" label="mitokmer Results" name="results" from_work_dir="results.csv"/>
    </outputs>
    <tests>
        <test>
         <param name="reads_select" value="single" />
         <param name="allreads" value="1a.fasta" format="fasta"/>
         <output name="output1" file="output/mitokmer_result.csv"/>
        </test>
    </tests>

    <help><![CDATA[