view macro.xml @ 0:33463c79e697 draft

planemo upload for repository commit deb581240339f3198dc23019e4445e8983ffa6ab
author iuc
date Sat, 13 Jan 2018 09:02:31 -0500
children 60ffb465aa4d
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<?xml version="1.0"?>
  <xml name="requirements">
      <requirement type="package" version="0.5.6">mykrobe</requirement>

  <token name="@select_inputs@">
         #set $name='sample'
         #set $type='fastq'
         ## Adding sample name, indicate specie and inputs fastq(s) files
          #if $data_type.type == "paired":

            ln -s '$data_type.fastq_input1' sample_1.fastq &&
            ln -s '$data_type.fastq_input2' sample_2.fastq &&

        #elif $data_type.type == "collection":
            #set $name=str($
            ln -s '$data_type.fastq_input1.forward' '$'_1.fastq &&
            ln -s '$data_type.fastq_input1.reverse' '$'_2.fastq &&

        #elif $data_type.type == "single":

            #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'):
              ln -s '$data_type.fastq_input1' sample.fastq &&

            #end if

            #if $data_type.fastq_input1.is_of_type('bam'):
              ln -s '$data_type.fastq_input1' sample.bam &&
              #set $type='bam'
            #end if

        #end if

  <xml name="inputs">
    <conditional name="data_type">
      <param name="type" type="select" label="Specify the read type.">
        <option value="single">Single-end Data</option>
        <option value="paired">Paired-end Data</option>
        <option value="collection">Collection Paired-end Data</option>
      <when value="single">
        <param name="fastq_input1" type="data" format="fastqsanger, fastq,fasta,bam" label="Single end read file(s)"/>
      <when value="paired">
        <param name="fastq_input1" type="data" format="fastqsanger, fastq" label="Forward paired-end read file"/>
        <param name="fastq_input2" type="data" format="fastqsanger, fastq" label="Reverse paired-end read file"/>
      <when value="collection">
        <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger, fastq" collection_type="paired" />

  <token name="@ATTRIBUTION@">
             **MyKrobe predict - Antibiotic resistance predictions**
             Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
             using Bruijn graph.

  <xml name="citation">
      <citation type="doi">10.1038/ncomms10063</citation>