view vcfleftalign.xml @ 4:50cf7cabae50 draft default tip

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

<tool id="vcfleftalign" name="VCFleftAlign:" version="@WRAPPER_VERSION@+galaxy0">
  <description>Left-align indels and complex variants in VCF dataset</description>
  <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>
    <test>
      <param name="reference_source_selector" value="history" />
      <param name="input_vcf" value="vcflib-phix.vcf"/>
      <param name="ref_file" value="vcflib-test-genome-phix.fa" />
      <param name="window_size" value="150" />
      <output name="out_file1" file="vcfleftalign-test1.vcf"/>
    </test>
    </tests>
  <help>

Left-aligns variants in VCF dataset.  Window size is determined dynamically according to the entropy of the regions flanking the indel.  These must have entropy > 1 bit/bp, or be shorter than ~5kb.

----

Vcfleftalign @IS_PART_OF_VCFLIB@
</help>
  <expand macro="citations" />
</tool>