comparison snp_caller_caller.xml @ 23:5db0545b9004 draft

update to v0.1.7.3

22:24154c580718

<tool id="variant_calling" name="Variant Calling" version="0.1.7.2">
  <description>From a reference and aligned reads generate a BCF file with position-specific variant likelihoods and coverage information</description>
  <macros>
    <import>toolshed_macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <version_command>python3 -m MiModD version -q</version_command>
  <command>
	python3 -m MiModD varcall

	"$ref_genome"

    --verbose
    --quiet
  </command>

  <inputs>
    <param name="ref_genome" type="data" format="fasta" label="reference genome" />
    <repeat name="list_input" title="Aligned reads input source" default="1" min="1">
      <param name="inputfile" type="data" format="bam" label="input file" />
    </repeat>
    <param name="group_by_id" type="boolean" label="group reads based on read group id only" truevalue="-i" falsevalue="" checked="false" help="If selected, this option ensures that only the read group id (but not the sample name) is considered in grouping reads in the input file(s). If turned off, read groups with identical sample names are automatically pooled and analyzed together even if they come from different NGS runs." />
    <param name="no_md5_check" type="boolean" label="turn off md5 sum verification" truevalue="-x" falsevalue="" checked="false" help="leave turned on to avoid accidental variant calling against a wrong reference genome version (see the tool help below)." />
    <param name="depth" type="integer" value="250" label="maximum per-BAM depth (default: 250)" help="to avoid excessive use of memory"/>
  </inputs>

  <outputs>
    <data name="output_vcf" format="bcf" label="Variant Calls from MiModd Variant Calling on ${on_string}"/>
  </outputs>

<help>
.. class:: infomark

23:5db0545b9004

<tool id="variant_calling" name="Variant Calling" version="0.1.7.3">
  <description>From a reference and aligned reads generate a BCF file with position-specific variant likelihoods and coverage information</description>
  <macros>
    <import>toolshed_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <version_command>python3 -m MiModD version -q</version_command>
  <command>
	python3 -m MiModD varcall

	"$ref_genome"

    --verbose
    --quiet
  </command>

  <inputs>
    <param format="fasta" label="reference genome" name="ref_genome" type="data" />
    <repeat default="1" min="1" name="list_input" title="Aligned reads input source">
      <param format="bam" label="input file" name="inputfile" type="data" />
    </repeat>
    <param checked="false" falsevalue="" help="If selected, this option ensures that only the read group id (but not the sample name) is considered in grouping reads in the input file(s). If turned off, read groups with identical sample names are automatically pooled and analyzed together even if they come from different NGS runs." label="group reads based on read group id only" name="group_by_id" truevalue="-i" type="boolean" />
    <param checked="false" falsevalue="" help="leave turned on to avoid accidental variant calling against a wrong reference genome version (see the tool help below)." label="turn off md5 sum verification" name="no_md5_check" truevalue="-x" type="boolean" />
    <param help="to avoid excessive use of memory" label="maximum per-BAM depth (default: 250)" name="depth" type="integer" value="250" />
  </inputs>

  <outputs>
    <data format="bcf" label="Variant Calls from MiModd Variant Calling on ${on_string}" name="output_vcf" />
  </outputs>

<help>
.. class:: infomark