comparison vcfgeno2haplo.xml @ 4:a3dea556218d draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo commit 36e9065027cc7bf721e9d203208477ee88906c57"

3:b890055e07bd

  <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    
  vcfgeno2haplo ${output_option} -w ${window_size} -r "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command>
  <inputs>
    <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>

       <when value="cached">
         <param name="ref_file" type="select" label="Select reference genome">
           <options from_data_table="fasta_indexes">
             <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
           </options>
	   <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
         </param>
	 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset">
	   <!-- Validators are commented to allow users apply too to any build. May need to be revised in the future
		<validator type="unspecified_build" />
		<validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
	   -->
	 </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
	 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" />
       </when>
     </conditional>
     <param name="window_size" type="text" value="30" label="compare records up to this many bp away" help="--window-size option (default = 30)" />
     <param name="output_option" type="boolean" truevalue="-o" falsevalue="" label="What to report?" help="--only-variants option" />
<!--       <option value=" ">Output entire haplotype</option>
       <option value="-o">Don't output the entire haplotype, just concatenate REF/ALT strings (delimited by &quot;:&quot;)</option>
     </param> -->
  </inputs>
  <outputs>
    <data format="vcf" name="out_file1" />

      <param name="window_size" value="5000" />
      <param name="input_vcf" value="vcflib-phix.vcf"/>
      <param name="ref_file" value="vcflib-test-genome-phix.fa" />
      <output name="out_file1" file="vcfgeno2haplo-test1.vcf"/>
    </test>
    </tests>
  <help>

Convert genotype-based phased alleles within a window size specified by -w option into haplotype alleles. Will break haplotype construction when encountering non-phased genotypes on input.

The options are::

4:a3dea556218d

  <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    
  vcfgeno2haplo ${output_option} -w ${window_size} -r "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"
  ]]></command>
  <inputs>
    <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>

       <when value="cached">
         <param name="ref_file" type="select" label="Select reference genome">
           <options from_data_table="fasta_indexes">
             <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
           </options>
           <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
         </param>
         <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset">
           <!-- Validators are commented to allow users apply too to any build. May need to be revised in the future
           <validator type="unspecified_build" />
           <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
           -->
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
         <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" />
       </when>
     </conditional>
     <param name="window_size" type="text" value="30" label="compare records up to this many bp away" help="--window-size option (default = 30)" />
     <param name="output_option" type="boolean" truevalue="-o" falsevalue="" label="What to report?" help="--only-variants option" />
     <!-- <option value=" ">Output entire haplotype</option>
       <option value="-o">Don't output the entire haplotype, just concatenate REF/ALT strings (delimited by &quot;:&quot;)</option>
     </param> -->
  </inputs>
  <outputs>
    <data format="vcf" name="out_file1" />

      <param name="window_size" value="5000" />
      <param name="input_vcf" value="vcflib-phix.vcf"/>
      <param name="ref_file" value="vcflib-test-genome-phix.fa" />
      <output name="out_file1" file="vcfgeno2haplo-test1.vcf"/>
    </test>
  </tests>
  <help>

Convert genotype-based phased alleles within a window size specified by -w option into haplotype alleles. Will break haplotype construction when encountering non-phased genotypes on input.

The options are::