comparison cpo_snippy.xml @ 5:698579246d0d draft

planemo upload

4:bd6f5844d60e

<tool id="snippy" name="snippy" version="3.2">
  <requirements>
    <requirement type="package" version="3.2">snippy</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" />

      gunzip out/snps.depth.gz

      &&

      tar -czf out.tgz out


    ]]>
  </command>
  <inputs>

5:698579246d0d

<tool id="cpo_snippy" name="CPO_Snippy" version="3.2">
  <description>Modified Snippy v3.2 to support contig inputs for the cpo_prediction workflow</description>
  <requirements>
    <requirement type="package" version="3.2">snippy</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" />

      gunzip out/snps.depth.gz

      &&

      #import re
      #set $dir_name = re.sub('[^\w_]', '_', $input.element_identifier)
      mkdir -p ${dir_name}/reference && cp out/snps.tab out/snps.aligned.fa ${dir_name}/ && cp out/reference/ref.fa ${dir_name}/reference/ &&

      tar -czf out.tgz ${dir_name}


    ]]>
  </command>
  <inputs>