comparison bwa-mem.xml @ 6:09a7281d24c5 draft

planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty

5:fbf460831036

<?xml version="1.0"?>
<tool id="bwa_mem" name="Map with BWA-MEM" version="0.3">
  <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
  <macros>
    <import>read_group_macros.xml</import>
    <import>bwa_macros.xml</import>
  </macros>
  <requirements>
    <requirement type="package" version="0.7.10.039ea20639">bwa</requirement>
    <requirement type="package" version="1.1">samtools</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" />
  </stdio>
  <command>
    #set $reference_fasta_filename = "localref.fa"

    #if str( $reference_source.reference_source_selector ) == "history":
        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;

      </when>
    </conditional>
  </inputs>

  <outputs>
    <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)"/>
  </outputs>

  <tests>
    <test>
      <param name="reference_source_selector" value="history" />

6:09a7281d24c5

<?xml version="1.0"?>
<tool id="bwa_mem" name="Map with BWA-MEM" version="0.3.1">
  <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
  <macros>
    <import>read_group_macros.xml</import>
    <import>bwa_macros.xml</import>
  </macros>
  <requirements>
    <requirement type="package" version="0.7.10.039ea20639">bwa</requirement>
    <requirement type="package" version="1.1">samtools</requirement>
  </requirements>
  <expand macro="stdio" />
  <command>
    #set $reference_fasta_filename = "localref.fa"

    #if str( $reference_source.reference_source_selector ) == "history":
        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;

      </when>
    </conditional>
  </inputs>

  <outputs>
    <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)">
      <expand macro="dbKeyActionsBwaMem" />
    </data>
  </outputs>

  <tests>
    <test>
      <param name="reference_source_selector" value="history" />