comparison discosnp_pp.xml @ 5:fd98c5af5a6c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"

4:912d042e4f1e

<?xml version='1.0' encoding='utf-8'?>
<tool profile="16.04" id="discosnp_pp" name="DiscoSnp++" version="@DISCOSNP_VERSION@">
    <description>is an efficient tool for detecting SNPs without a reference genome.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="discosnp_requirements" />
    <command><![CDATA[
        ## simple option
        #if str( $input_type_options.input_type) == "single"
            @discosnp_single_reads@
        ## paired option
        #else if str( $input_type_options.input_type) == "paired"
            @discosnp_paired_reads@
        ## mix option
        #else
            @discosnp_single_reads@
            @discosnp_paired_reads@
        #end if

        #if str($VCF_option.mapping) == 'reference'
            #set $reference_file = os.path.basename(str($VCF_option.G)) + "." + $VCF_option.G.ext
            ln -sf '${VCF_option.G}' '${reference_file}' &&
        #end if

        run_discoSnp++.sh
        @discosnp_inputs@
        ${T}
        -b ${b}
        #if str($VCF_option.mapping) == 'reference'
            -G '${reference_file}'
            ${VCF_option.R}
        #end if

        --max_threads \${GALAXY_SLOTS:-1}

  ]]></command>

  <inputs>


      <expand macro="discosnp_inputs" />

      <param argument="-b" type="select" label="Branching strategy">
          <option value="0">variants for which any of the two paths is branching are discarded</option>
          <option value="1">forbid SNPs for wich the two paths are branching</option>
          <option value="2">No limitation on branching</option>
      </param>

      <expand macro="discosnp_options" />

      <param argument="-T" type="boolean" checked="false" truevalue="-T" falsevalue="" label="Extends each polymorphism with left and right contigs" />

      <conditional name="VCF_option" >
          <param name="mapping" type="select" label="VCF option">
              <option value="default">Do not use reference genome</option>
              <option value="reference">Mapping with a reference genome</option>
          </param>
          <when value="default"></when>
          <when value="reference">
              <param argument="-G" type="data" format="fasta,fastq" label="Reference genome file" />
              <param argument="-R" type="boolean" truevalue="-R" falsevalue="" checked="false" label="Use the reference genome also in the variant calling, not only for mapping results" />
          </when>
      </conditional>

  </inputs>

  <outputs>
      <data name="vcf" from_work_dir="*_coherent.vcf" format="vcf" label="VCF with ${tool.name} on $on_string"/>
      <data name="fasta" from_work_dir="*_coherent.fa" format="fasta" label="Multifasta with ${tool.name} on $on_string"/>
  </outputs>

  <tests>
      <test>
          <conditional name="input_type_options">
              <param name="input_type" value="single"/>
              <param name="list_reads" value="discosnp/reads1,discosnp/reads2" ftype="fasta" />
          </conditional>
          <param name="k" value="25"/>
          <output name="fasta" file="discosnp/multifasta.fa"/>
          <output name="vcf" file="discosnp/vcf_file.vcf" compare="diff" lines_diff="2"/>
      </test>

              <param name="input_type" value="paired"/>
              <param name="list_paired_reads">
                  <collection type="list:paired">
                      <element name="Pair1">
                          <collection type="paired">
                              <element name="forward" value="discosnp/reads1" ftype="fasta"/>
                              <element name="reverse" value="discosnp/reads2" ftype="fasta"/>
                          </collection>
                      </element>
                  </collection>
              </param>
          </conditional>
          <conditional name="VCF_option">
              <param name="mapping" value="reference"/>
              <param name="G" value="discosnp/reads1" ftype="fasta"/>
          </conditional>
          <output name="fasta" file="discosnp/multifasta_paired.fa"/>
          <output name="vcf" file="discosnp/vcf_file_paired.vcf" compare="diff" lines_diff="2"/>
      </test>
  </tests>

  <help><![CDATA[

**Description**

Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).

5:fd98c5af5a6c

<tool id="discosnp_pp" name="DiscoSnp++" version="@DISCOSNP_VERSION@+galaxy0" profile="@PROFILE@">
    <description>is an efficient tool for detecting SNPs without a reference genome.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="discosnp_requirements" />
    <command detect_errors="exit_code"><![CDATA[
        #if str($input_type_options.input_type) == "single":
            @discosnp_single_for@
            @single_reads@
            @discosnp_single_end_for@
        #else if str($input_type_options.input_type) == "paired":
            @discosnp_paired_for@
            @paired_reads@
            @discosnp_paired_end_for@
        #else:
            @discosnp_single_for@
            @single_reads@
            @discosnp_single_end_for@
            @discosnp_paired_for@
            @paired_reads@
            @discosnp_paired_end_for@
        #end if
        #if str($VCF_option.mapping) == 'reference':
            #set $reference_file = os.path.basename(str($VCF_option.G)) + "." + $VCF_option.G.ext
            ln -sf '${VCF_option.G}' '${reference_file}' &&
        #end if
        run_discoSnp++.sh
        @discosnp_inputs@
        ${T}
        -b ${b}
        #if str($VCF_option.mapping) == 'reference':
            -G '${reference_file}'
            ${VCF_option.R}
        #end if
        --max_threads \${GALAXY_SLOTS:-1}
  ]]></command>
  <inputs>
      <expand macro="discosnp_inputs" />
      <param argument="-b" type="select" label="Branching strategy">
          <option value="0">variants for which any of the two paths is branching are discarded</option>
          <option value="1">forbid SNPs for wich the two paths are branching</option>
          <option value="2">No limitation on branching</option>
      </param>
      <expand macro="discosnp_options" />
      <param argument="-T" type="boolean" checked="false" truevalue="-T" falsevalue="" label="Extends each polymorphism with left and right contigs" />
      <conditional name="VCF_option" >
          <param name="mapping" type="select" label="VCF option">
              <option value="default">Do not use reference genome</option>
              <option value="reference">Mapping with a reference genome</option>
          </param>
          <when value="default"></when>
          <when value="reference">
              <param argument="-G" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Reference genome file" />
              <param argument="-R" type="boolean" truevalue="-R" falsevalue="" checked="false" label="Use the reference genome also in the variant calling, not only for mapping results" />
          </when>
      </conditional>
  </inputs>
  <outputs>
      <data name="vcf" from_work_dir="*_coherent.vcf" format="vcf" label="VCF with ${tool.name} on $on_string"/>
      <data name="fasta" from_work_dir="*_coherent.fa" format="fasta" label="Multifasta with ${tool.name} on $on_string"/>
  </outputs>
  <tests>
      <test>
          <conditional name="input_type_options">
              <param name="input_type" value="single"/>
              <param name="list_reads" value="discosnp/reads1.gz,discosnp/reads2.gz" ftype="fasta.gz" />
          </conditional>
          <param name="k" value="25"/>
          <output name="fasta" file="discosnp/multifasta.fa"/>
          <output name="vcf" file="discosnp/vcf_file.vcf" compare="diff" lines_diff="2"/>
      </test>

              <param name="input_type" value="paired"/>
              <param name="list_paired_reads">
                  <collection type="list:paired">
                      <element name="Pair1">
                          <collection type="paired">
                              <element name="forward" value="discosnp/reads1.gz" ftype="fasta.gz"/>
                              <element name="reverse" value="discosnp/reads2.gz" ftype="fasta.gz"/>
                          </collection>
                      </element>
                  </collection>
              </param>
          </conditional>
          <conditional name="VCF_option">
              <param name="mapping" value="reference"/>
              <param name="G" value="discosnp/reads1.gz" ftype="fasta.gz"/>
          </conditional>
          <output name="fasta" file="discosnp/multifasta_paired.fa"/>
          <output name="vcf" file="discosnp/vcf_file_paired.vcf" compare="diff" lines_diff="2"/>
      </test>
  </tests>
  <help><![CDATA[

**Description**

Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).