comparison vcfcheck.xml @ 2:265e5230925c draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcheck commit 0b9b6512272b82637c2f1e831367e89aed77ae79

1:ef00ee1f1842

<tool id="vcfcheck" name="VCFcheck:" version="0.0.3">
  <description>Verify that the reference allele matches the reference genome</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"></expand>
  <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    
  vcfcheck $failure_selector -f "${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>
       </param>
       <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="failure_selector" type="select" display="radio" label="Exclude or include failed sites">
       <option value="-x">Exculde failures (-x option)</option>
       <option value="-k">Keep failures (-k option)</option>
     </param>
  </inputs>
  <outputs>
    <data format="vcf" name="out_file1" />
  </outputs>
  <stdio>
    <regex match="index file" source="stderr" level="warning"/>
  </stdio>
  <tests>
    <test>
      <param name="reference_source_selector" value="history" />
      <param name="failure_selection" value="-x" />
      <param name="input_vcf" value="vcflib-phix.vcf"/>
      <param name="ref_file" value="vcflib-test-genome-phix.fa" />
      <output name="out_file1" file="vcfcheck-test1.vcf"/>
    </test>
    </tests>
  <help>

Verifies that the VCF REF field matches the reference as described.  

The options are::

    -k, --keep-failures    Print if the record fails, otherwise not.

----

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

2:265e5230925c

<tool id="vcfcheck" name="VCFcheck:" version="@WRAPPER_VERSION@.0">
    <description>Verify that the reference allele matches the reference genome</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"></expand>
    <stdio>
        <regex match="index file" source="stderr" level="warning"/>
    </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
        vcfcheck $failure_selector -f "${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>
            </param>
            <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="failure_selector" type="select" display="radio" label="Exclude or include failed sites">
            <option value="-x">Exculde failures (-x option)</option>
            <option value="-k">Keep failures (-k option)</option>
        </param>
    </inputs>
    <outputs>
        <data format="vcf" name="out_file1" />
    </outputs>
    <tests>
        <test>
            <param name="reference_source_selector" value="history" />
            <param name="failure_selection" value="-x" />
            <param name="input_vcf" value="vcflib-phix.vcf"/>
            <param name="ref_file" value="vcflib-test-genome-phix.fa" />
            <output name="out_file1" file="vcfcheck-test1.vcf"/>
        </test>
    </tests>
    <help>

Verifies that the VCF REF field matches the reference as described.  

The options are::

    -k, --keep-failures    Print if the record fails, otherwise not.

----

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