comparison vcfprimers.xml @ 4:17096387c0e6 draft default tip

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

3:d226a7327946

  <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( $reference_source.ref_file.fields.path )
    #end if    
   vcfprimers -f "${reference_fasta_filename}" -l "${primer_length}" "${input_vcf}" > "${out_file1}"</command>
  <inputs>
<param name="input_vcf" type="data" format="vcf" label="VCF dataset to extract flanks" />
    <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>

       </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>

4:17096387c0e6

  <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( $reference_source.ref_file.fields.path )
    #end if    
   vcfprimers -f '${reference_fasta_filename}' -l "${primer_length}" '${input_vcf}' > '${out_file1}'
  ]]></command>
  <inputs>
<param name="input_vcf" type="data" format="vcf" label="VCF dataset to extract flanks" />
    <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>

       </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>