comparison varextract.xml @ 23:5db0545b9004 draft

update to v0.1.7.3

22:24154c580718

<tool id="extract_variants" name="Extract Variant Sites" version="0.1.7.2">
  <description>from a BCF file</description>
  <macros>
    <import>toolshed_macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <version_command>python3 -m MiModD version -q</version_command>
  <command>
	python3 -m MiModD varextract "$ifile"
	#if $len($sitesinfo)
	    -p
	    #for $source in $sitesinfo
            "${source.pre_vcf}"

	$keep_alts
	--verbose
  </command>

  <inputs>
      <param name="ifile" type="data" format="bcf" label="BCF input file" help="Use the Variant Calling tool to generate the input for this tool."/>
      <repeat name="sitesinfo" title="include information from pre-calculated vcf file" default="0">
	      <param name="pre_vcf" type="data" format="vcf" label="independently generated vcf file" />
      </repeat>
      <param name="keep_alts" type="boolean" label="keep all sites with alternate bases" truevalue="-a" falsevalue="" checked="false" help="If selected, the VCF output will include ALL sites for which non-reference bases have been observed, i.e., even those not considered allelic sites by the variant caller." />
  </inputs>
  <outputs>
    <data name="output_vcf" format="vcf" label="Variants extracted with MiModd from ${on_string}"/>
  </outputs>

<help>
.. class:: infomark

23:5db0545b9004

<tool id="extract_variants" name="Extract Variant Sites" version="0.1.7.3">
  <description>from a BCF file</description>
  <macros>
    <import>toolshed_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <version_command>python3 -m MiModD version -q</version_command>
  <command> 
	python3 -m MiModD varextract "$ifile"
	#if $len($sitesinfo)
	    -p
	    #for $source in $sitesinfo
            "${source.pre_vcf}"

	$keep_alts
	--verbose
  </command>

  <inputs>
      <param format="bcf" help="Use the Variant Calling tool to generate the input for this tool." label="BCF input file" name="ifile" type="data" />
      <repeat default="0" name="sitesinfo" title="include information from pre-calculated vcf file">
	      <param format="vcf" label="independently generated vcf file" name="pre_vcf" type="data" />
      </repeat>
      <param checked="false" falsevalue="" help="If selected, the VCF output will include ALL sites for which non-reference bases have been observed, i.e., even those not considered allelic sites by the variant caller." label="keep all sites with alternate bases" name="keep_alts" truevalue="-a" type="boolean" />
  </inputs>
  <outputs>
    <data format="vcf" label="Variants extracted with MiModd from ${on_string}" name="output_vcf" />
  </outputs>

<help>
.. class:: infomark