comparison vcfleftalign.xml @ 4:29f9b782727e draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign commit 36e9065027cc7bf721e9d203208477ee88906c57"

3:d2406f98a782

  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="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;
    #else:
       #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
    #end if    
   vcfleftalign -r "${reference_fasta_filename}" -w "${window_size}" "${input_vcf}" > "${out_file1}"</command>
  <inputs>
<param name="input_vcf" type="data" format="vcf" label="VCF dataset to left-align" />
    <conditional name="reference_source">
       <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
         <option value="cached">Locally cached</option>
         <option value="history">History</option>
       </param>
       <when value="cached">
         <param name="ref_file" type="select" label="Select reference genome">
           <options from_data_table="fasta_indexes">
           </options>
	   <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
       </when>
     </conditional>
     <param name="window_size" type="integer" value="150" label="Use a window of this many bp when left-aligning" help="default = 150 bp" />
  </inputs>
  <outputs>
    <data format="vcf" name="out_file1" />
  </outputs>
  <tests>

4:29f9b782727e

  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio" />
  <command><![CDATA[
    #set $reference_fasta_filename = "localref.fa"
    #if str( $reference_source.reference_source_selector ) == "history":
       ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
    #else:
       #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
    #end if    
   vcfleftalign -r '${reference_fasta_filename}' -w "${window_size}" '${input_vcf}' > '${out_file1}'
  ]]></command>
  <inputs>
    <param name="input_vcf" type="data" format="vcf" label="VCF dataset to left-align" />
      <conditional name="reference_source">
        <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
          <option value="cached">Locally cached</option>
          <option value="history">History</option>
        </param>
        <when value="cached">
          <param name="ref_file" type="select" label="Select reference genome">
            <options from_data_table="fasta_indexes">
            </options>
            <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
          </param>
        </when>
        <when value="history"> <!-- FIX ME!!!! -->
          <param name="ref_file" type="data" format="fasta" label="Using reference file" />
        </when>
      </conditional>
    <param name="window_size" type="integer" value="150" label="Use a window of this many bp when left-aligning" help="default = 150 bp" />
  </inputs>
  <outputs>
    <data format="vcf" name="out_file1" />
  </outputs>
  <tests>