comparison bowtie_wrapper.xml @ 5:306077e393d4 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit b2e1043bf4db38be490fec298a1829f8e4a1c48e

4:df86f29bedee

<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.3">
  <requirements>
    <requirement type="package" version="0.12.7">bowtie</requirement>
  </requirements>
  <description></description>
  <version_command>bowtie --version</version_command>
  <command interpreter="python">
    bowtie_wrapper.py

          #end if
          --offrate="${singlePaired.pParams.pOffrate}"
          --seed="${singlePaired.pParams.pSeed}"
        #end if
      #end if
  </command>
  <inputs>
    <conditional name="refGenomeSource">
      <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
        <option value="indexed">Use a built-in index</option>

            <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
          </when> <!-- full -->
        </conditional> <!-- pParams -->
      </when> <!-- paired -->
    </conditional> <!-- singlePaired -->
    <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file (--sam-nohead)" help="Bowtie produces SAM with several lines of header information by default" />
  </inputs>
  <outputs>
    <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
      <actions>

              <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
            </action>
          </when>
        </conditional>
      </actions>
    </data>
    <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
      <filter>((
          singlePaired['sPaired'] == "single" and
          singlePaired['sParams']['sSettingsType'] == "full" and

      <param name="index" value="equCab2chrM" />
      <param name="sPaired" value="single" />
      <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
      <param name="sSettingsType" value="preSet" />
      <param name="suppressHeader" value="true" />
      <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True" />
    </test>
    <test>
      <!--
      Bowtie command:
      bowtie-build -f test-data/phiX.fasta phiX_base

      <param name="sMaxFile" value="false" />
      <param name="sBest" value="noBest" />
      <param name="sOffrate" value="-1" />
      <param name="sSeed" value="-1" />
      <param name="suppressHeader" value="true" />
      <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True" />
    </test>
    <test>
      <!--
      Bowtie command:
      bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base

      <param name="pMaxInsert" value="1000" />
      <param name="pMateOrient" value="ff" />
      <param name="pSettingsType" value="preSet" />
      <param name="suppressHeader" value="true" />
      <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" />
    </test>
  </tests>

  <help>

5:306077e393d4

<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.5">
  <requirements>
    <requirement type="package" version="1.1.2">bowtie</requirement>
  </requirements>
  <description></description>
  <version_command>bowtie --version</version_command>
  <command interpreter="python">
    bowtie_wrapper.py

          #end if
          --offrate="${singlePaired.pParams.pOffrate}"
          --seed="${singlePaired.pParams.pSeed}"
        #end if
      #end if
      #if $save_mapping_stats
        --output_mapping_stats="$mapping_stats"
      #end if
  </command>
  <inputs>
    <conditional name="refGenomeSource">
      <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
        <option value="indexed">Use a built-in index</option>

            <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
          </when> <!-- full -->
        </conditional> <!-- pParams -->
      </when> <!-- paired -->
    </conditional> <!-- singlePaired -->
    <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie mapping statistics to the history" />
    <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file (--sam-nohead)" help="Bowtie produces SAM with several lines of header information by default" />
  </inputs>
  <outputs>
    <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
      <actions>

              <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
            </action>
          </when>
        </conditional>
      </actions>
    </data>
    <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
      <filter>save_mapping_stats is True</filter>
    </data>
    <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
      <filter>((
          singlePaired['sPaired'] == "single" and
          singlePaired['sParams']['sSettingsType'] == "full" and

      <param name="index" value="equCab2chrM" />
      <param name="sPaired" value="single" />
      <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
      <param name="sSettingsType" value="preSet" />
      <param name="suppressHeader" value="true" />
      <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True">
        <metadata name="dbkey" value="equCab2" />
      </output>
    </test>
    <test>
      <!--
      Bowtie command:
      bowtie-build -f test-data/phiX.fasta phiX_base

      <param name="sMaxFile" value="false" />
      <param name="sBest" value="noBest" />
      <param name="sOffrate" value="-1" />
      <param name="sSeed" value="-1" />
      <param name="suppressHeader" value="true" />
      <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True">
        <metadata name="dbkey" value="equCab2" />
      </output>
    </test>
    <test>
      <!--
      Bowtie command:
      bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base

      <param name="pMaxInsert" value="1000" />
      <param name="pMateOrient" value="ff" />
      <param name="pSettingsType" value="preSet" />
      <param name="suppressHeader" value="true" />
      <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" />
    </test>
    <test>
      <!--
      Bowtie command:
      bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base
      bowtie -q -X 1000 +ff -p 4 -S +sam-nohead phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out10_u.sam
      sort bowtie_out10_u.sam > bowtie_out10.sam
      -p is the number of threads. You need to replace the + with 2 dashes.
      chrM_base is the index files' location/base name.
      -->
      <param name="genomeSource" value="history" />
      <param name="ownFile" value="phiX.fasta" />
      <param name="indexSettings" value="indexFull" />
      <param name="autoB" value="auto" />
      <param name="nodc" value="dc" />
      <param name="noref" value="ref" />
      <param name="offrate" value="5" />
      <param name="ftab" value="10" />
      <param name="ntoa" value="no" />
      <param name="endian" value="little" />
      <param name="seed" value="-1" />
      <param name="sPaired" value="paired" />
      <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
      <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
      <param name="pMaxInsert" value="1000" />
      <param name="pMateOrient" value="ff" />
      <param name="pSettingsType" value="preSet" />
      <param name="suppressHeader" value="true" />
      <param name="save_mapping_stats" value="true" />
      <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" />
      <output name="mapping_stats" ftype="txt" file="bowtie_out11.txt" sort="True" />
    </test>
  </tests>

  <help>