annotate serotypefinder.xml @ 0:1577ee103ed1 draft default tip

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<tool id="serotypefinder" name="serotypefinder" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
    <requirements>
        <requirement type="package">serotypefinder</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

    #if $reads.reads_select == 'collection'
      #set $name = $reads.coll.name.replace(' ', '_')
      #set $forward = $reads.coll.forward
      #set $reverse = $reads.coll.reverse
      #set $infile = $name + "_1.fastq " +  $name + "_2.fastq" 
      #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
        gunzip -c $reverse > reverse.fastq;
        #set $reverse = './reverse.fastq'
        gunzip -c $forward > forward.fastq;
        #set $forward = './forward.fastq'
      #end if
      ln -s $forward ${name}_1.fastq;
      ln -s $reverse ${name}_2.fastq;
   #else 
      #set $name = $reads.assembly.name.replace(' ', '_')
      #set $ga = $reads.assembly
      #set $infile = $name + ".fasta" 
      ln -s $ga ${name}.fasta;
    #end if
    serotypefinder -x -i $infile

    ]]></command>
    <inputs>
        <conditional name="reads">
            <param name="reads_select" type="select" label="Genome assembly or paired-end collection">
                <option value="collection">Paired collection from your history</option>
                <option value="genome">Genome Assembly</option>
            </param>
            <when value="collection">
                <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
            </when>
            <when value="genome">
                <param label="Genome assembly" name="assembly" type="data" format="fasta"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="results" format="tabular" from_work_dir="results_tab.tsv" />
    </outputs>
  <help><![CDATA[
    Serotype predictions for E.coli.
  ]]></help>
    <citations>
       <citation type="bibtex">
         @misc{fleming,
         title={serotypefinder - Serotype Prediction for E. coli},
         journal={epub}, publisher={epub},
         author={Scheutz, Flemming},
         year={2023}, month={Max},
         url={https://bitbucket.org/genomicepidemiology/serotypefinder/src/master}},

       </citation>
    </citations>
</tool>