annotate mykrobe_genotype.xml @ 0:d783eb846f59 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab

<?xml version="1.0" encoding="utf-8"?>
<tool id="mykrobe_genotype" name="mkyrobe genotype" version="0.5.6" >
  <description>Antibiotic resistance predictions</description>
  <macros>
    <import>macro.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code">
<![CDATA[
        @select_inputs@

        mykrobe genotype 
        '$name'
        '$probe_set'

        #if $kmer:
          --kmer $kmer
        #end if

        #if $expected_depth:
          --expected_depth $expected_depth
        #end if


        -q
        -t "\${GALAXY_SLOTS:-1}"

        -1
        #if $type == 'fastq':
          *.fastq
        #elif $type == 'bam':
          *.bam
        #else
          *.fasta  
        #end if
         > $json
]]>
  </command>
  <inputs>
    <expand macro="inputs" />
    <param name="probe_set" type="data" format="fasta" label="Probe Set"/>
    <param name="kmer" argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/>
    <param name="expected_depth" argument="--expected_depth" optional="True" type="integer" min="0" label="Expected Depth"  help=""/>
  </inputs>
  <outputs>
    <data name="json" format="json" label="JSON prediction"/>
  </outputs>
  <tests>
    <test>
      <param name="type" value="single"/>
      <param name="fastq_input1" value="reads.fastq"/>
      <param name="probe_set" value="tb-bradley-probe-set-feb-09-2017.fasta.gz"/>
      <output name="json">
        <assert_contents>
          <has_text_matching expression="ref-S315T"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help>
@ATTRIBUTION@
  </help>
  <expand macro="citation" />
</tool>