comparison bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.xml @ 21:b49ad9f12dfa draft

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20:87b1fa00d6ab

<tool id="bowtie_rRNA_tRNA_removal_wrapper" name="Remove rRNA and tRNA using Bowtie" version="1.4.0">
  <description></description>
  <requirements>
    <requirement type="package" version="1.2.0">bowtie</requirement>
  </requirements>
  <version_command>bowtie --version</version_command>

  </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>
        <option value="history" selected="True">Use one from the history</option>
      </param>
      <when value="indexed">
        <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
          <options from_data_table="bowtie_indexes">
            <filter type="sort_by" column="2" />
            <validator type="no_options" message="No indexes are available" />
          </options>
        </param>
      </when>

            <param name="sForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)">
              <option value="forward">Align against the forward reference strand</option>
              <option value="noForward">Do not align against the forward reference strand</option>
            </param>
            <param name="sReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
              <option value="reverse">Align against the reverse-complement reference strand</option>
              <option value="noReverse" selected="true">Do not align against the reverse-complement reference strand</option>
            </param>
            <conditional name="sBestOption">
              <param name="sBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option">
                <option value="noBest">Do not use best</option>
                <option value="doBest">Use best</option>

                  <option value="round">Round to nearest 10</option>
                  <option value="noRound">Do not round to nearest 10</option>
                </param>
              </when>
              <when value="vMode">
                <param name="maxMismatches" type="integer" value="" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" />
                <param name="pSeedLen" type="integer" value="25" min="5" label="Seed length (-l)" help="Minimum value is 5" />
              </when>
            </conditional>
            <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" />
            <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)">
              <option value="forward">Align against the forward reference strand</option>
              <option value="noForward">Do not align against the forward reference strand</option>
            </param>
            <param name="pReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
              <option value="reverse">Align against the reverse-complement reference strand</option>
              <option value="noReverse" selected="true">Do not align against the reverse-complement reference strand</option>
            </param>
            <conditional name="pBestOption">
              <param name="pBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option">
                <option value="noBest">Do not use best</option>
                <option value="doBest">Use best</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="True" 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>
        <conditional name="refGenomeSource.genomeSource">
          <when value="indexed">
            <action type="metadata" name="dbkey">
              <option type="from_data_table" name="bowtie_indexes" column="1" offset="0">
                <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                <filter type="param_value" ref="refGenomeSource.index" column="0"/>
              </option>
            </action>
          </when>

      </actions>
    </data>
  </outputs>
  <tests>
    <test>
      <!--
      Bowtie command:
      bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam
      sort bowtie_out6_u.sam > bowtie_out6.sam
      -p is the number of threads. You need to replace the + with 2 dashes.
      chrM_base needs to be the base location/name of the index files.
      -->
      <param name="genomeSource" value="indexed" />
      <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
      <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
      bowtie -q -X 1000 +ff -p 4 -S +sam-nohead -n 2 -e 70 -l 28 +pairtries 100 +maxbts 800 +best +un bowtie_out8_u.fastq phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out7_u.sam
      sort bowtie_out7_u.sam > bowtie_out7.sam
      sort bowtie_out8_u_1.sam > bowtie_out8_1.sam
      sort bowtie_out8_u_2.sam > bowtie_out8_2.sam
      Then also need to modify bowtie_out8_1.sam and bowtie_out8_2.sam so that all @ lines come before sequence lines.
      -p is the number of threads. You need to replace the + with 2 dashes.
      The two unmapped output files will be named bowtie_out8_1.fastq and bowtie_out8_2.fastq.
      chrM_base is the index files' location/base name.
      -->
      <param name="genomeSource" value="history" />
      <param name="ownFile" value="phiX.fasta" />
      <param name="indexSettings" value="indexPreSet" />
      <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="full" />
      <param name="pSkip" value="0" />
      <param name="pAlignLimit" value="-1" />
      <param name="pTrimH" value="0" />
      <param name="pTrimL" value="0" />
      <param name="alignMode" value="nMode" />
      <param name="pMismatchSeed" value="2" />
      <param name="pMismatchQual" value="70" />
      <param name="pSeedLen" value="28" />
      <param name="pRounding" value="round" />
      <param name="pMinInsert" value="0" />
      <param name="pMaxAlignAttempt" value="100" />
      <param name="pForwardAlign" value="forward" />
      <param name="pReverseAlign" value="reverse" />
      <param name="pTryHard" value="noTryHard" />
      <param name="pValAlign" value="1" />
      <param name="pAllValAligns" value="noAllValAligns" />
      <param name="pSuppressAlign" value="-1" />
      <param name="pUnmappedFile" value="true" />
      <param name="pMaxFile" value="false" />
      <param name="pBest" value="doBest" />
      <param name="pdMaxBacktracks" value="800" />
      <param name="pdStrata" value="noStrata" />
      <param name="pOffrate" value="-1" />
      <param name="pSeed" value="-1" />
      <param name="suppressHeader" value="true" />
      <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
      <output name="output_unmapped_reads_l" ftype="fastqsanger" file="bowtie_out8_1.fastq" sort="True" />
      <output name="output_unmapped_reads_r" ftype="fastqsanger" file="bowtie_out8_2.fastq" sort="True" />
    </test>
    <!-- start testing of non-sanger variant fastq reads -->
    <test>
      <param name="genomeSource" value="history" />
      <param name="ownFile" value="phiX.fasta" />
      <param name="indexSettings" value="indexPreSet" />
      <param name="sPaired" value="paired" />
      <param name="pInput1" ftype="fastqillumina" value="bowtie_in5.fastqillumina" />
      <param name="pInput2" ftype="fastqillumina" value="bowtie_in6.fastqillumina" />
      <param name="pMaxInsert" value="1000" />
      <param name="pMateOrient" value="ff" />
      <param name="pSettingsType" value="full" />
      <param name="pSkip" value="0" />
      <param name="pAlignLimit" value="-1" />
      <param name="pTrimH" value="0" />
      <param name="pTrimL" value="0" />
      <param name="alignMode" value="nMode" />
      <param name="pMismatchSeed" value="2" />
      <param name="pMismatchQual" value="70" />
      <param name="pSeedLen" value="28" />
      <param name="pRounding" value="round" />
      <param name="pMinInsert" value="0" />
      <param name="pMaxAlignAttempt" value="100" />
      <param name="pForwardAlign" value="forward" />
      <param name="pReverseAlign" value="reverse" />
      <param name="pTryHard" value="noTryHard" />
      <param name="pValAlign" value="1" />
      <param name="pAllValAligns" value="noAllValAligns" />
      <param name="pSuppressAlign" value="-1" />
      <param name="pUnmappedFile" value="true" />
      <param name="pMaxFile" value="false" />
      <param name="pBest" value="doBest" />
      <param name="pdMaxBacktracks" value="800" />
      <param name="pdStrata" value="noStrata" />
      <param name="pOffrate" value="-1" />
      <param name="pSeed" value="-1" />
      <param name="suppressHeader" value="true" />
      <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
      <output name="output_unmapped_reads_l" ftype="fastqillumina" file="bowtie_out8_1.fastqillumina.sorted" sort="True" />
      <output name="output_unmapped_reads_r" ftype="fastqillumina" file="bowtie_out8_2.fastqillumina.sorted" sort="True" />
    </test>
    <test>
      <param name="genomeSource" value="history" />
      <param name="ownFile" value="phiX.fasta" />
      <param name="indexSettings" value="indexPreSet" />
      <param name="sPaired" value="paired" />
      <param name="pInput1" ftype="fastqsolexa" value="bowtie_in5.fastqsolexa" />
      <param name="pInput2" ftype="fastqsolexa" value="bowtie_in6.fastqsolexa" />
      <param name="pMaxInsert" value="1000" />
      <param name="pMateOrient" value="ff" />
      <param name="pSettingsType" value="full" />
      <param name="pSkip" value="0" />
      <param name="pAlignLimit" value="-1" />
      <param name="pTrimH" value="0" />
      <param name="pTrimL" value="0" />
      <param name="alignMode" value="nMode" />
      <param name="pMismatchSeed" value="2" />
      <param name="pMismatchQual" value="70" />
      <param name="pSeedLen" value="28" />
      <param name="pRounding" value="round" />
      <param name="pMinInsert" value="0" />
      <param name="pMaxAlignAttempt" value="100" />
      <param name="pForwardAlign" value="forward" />
      <param name="pReverseAlign" value="reverse" />
      <param name="pTryHard" value="noTryHard" />
      <param name="pValAlign" value="1" />
      <param name="pAllValAligns" value="noAllValAligns" />
      <param name="pSuppressAlign" value="-1" />
      <param name="pUnmappedFile" value="true" />
      <param name="pMaxFile" value="false" />
      <param name="pBest" value="doBest" />
      <param name="pdMaxBacktracks" value="800" />
      <param name="pdStrata" value="noStrata" />
      <param name="pOffrate" value="-1" />
      <param name="pSeed" value="-1" />
      <param name="suppressHeader" value="true" />
      <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
      <output name="output_unmapped_reads_l" ftype="fastqsolexa" file="bowtie_out8_1.fastqsolexa.sorted" sort="True" />
      <output name="output_unmapped_reads_r" ftype="fastqsolexa" file="bowtie_out8_2.fastqsolexa.sorted" sort="True" />
    </test>
    <!-- end testing of non-sanger variant fastq reads -->
    <test>
      <!--
      Bowtie command:
      bowtie -q -p 4 -S +sam-nohead -n 2 -e 70 -l 28 -y -k 1 chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out9_u.sam
      sort bowtie_out9_u.sam > bowtie_out9.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="indexed" />
      <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
      <param name="index" value="equCab2chrM" />
      <param name="sPaired" value="single" />
      <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
      <param name="sSettingsType" value="full" />
      <param name="sSkip" value="0" />
      <param name="sAlignLimit" value="-1" />
      <param name="sTrimH" value="0" />
      <param name="sTrimL" value="0" />
      <param name="alignMode" value="nMode" />
      <param name="sMismatchSeed" value="2" />
      <param name="sMismatchQual" value="70" />
      <param name="sSeedLen" value="28" />
      <param name="sRounding" value="round" />
      <param name="sForwardAlign" value="forward" />
      <param name="sReverseAlign" value="reverse" />
      <param name="sTryHard" value="doTryHard" />
      <param name="sValAlign" value="1" />
      <param name="sAllValAligns" value="noAllValAligns" />
      <param name="sSuppressAlign" value="-1" />
      <param name="sUnmappedFile" value="false" />
      <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
      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" />
      <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>

**What it does**

21:b49ad9f12dfa

<tool id="bowtie_rRNA_tRNA_removal_wrapper" name="Remove rRNA and tRNA using Bowtie" version="1.5.0">
  <description></description>
  <requirements>
    <requirement type="package" version="1.2.0">bowtie</requirement>
  </requirements>
  <version_command>bowtie --version</version_command>

  </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>
        <option value="history">Use one from the history</option>
      </param>
      <when value="indexed">
        <param name="index" type="select" label="Select a reference index" help="if your index of interest is not listed - contact Galaxy team">
          <options from_data_table="bowtie_rRNA_indexes">
            <filter type="sort_by" column="2" />
            <validator type="no_options" message="No indexes are available" />
          </options>
        </param>
      </when>

            <param name="sForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)">
              <option value="forward">Align against the forward reference strand</option>
              <option value="noForward">Do not align against the forward reference strand</option>
            </param>
            <param name="sReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
              <option value="reverse" selected="true">Align against the reverse-complement reference strand</option>
              <option value="noReverse">Do not align against the reverse-complement reference strand</option>
            </param>
            <conditional name="sBestOption">
              <param name="sBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option">
                <option value="noBest">Do not use best</option>
                <option value="doBest">Use best</option>

                  <option value="round">Round to nearest 10</option>
                  <option value="noRound">Do not round to nearest 10</option>
                </param>
              </when>
              <when value="vMode">
                <param name="maxMismatches" type="integer" value="3" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" />
                <param name="pSeedLen" type="integer" value="25" min="5" label="Seed length (-l)" help="Minimum value is 5" />
              </when>
            </conditional>
            <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" />
            <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)">
              <option value="forward">Align against the forward reference strand</option>
              <option value="noForward">Do not align against the forward reference strand</option>
            </param>
            <param name="pReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
              <option value="reverse" selected='true'>Align against the reverse-complement reference strand</option>
              <option value="noReverse">Do not align against the reverse-complement reference strand</option>
            </param>
            <conditional name="pBestOption">
              <param name="pBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option">
                <option value="noBest">Do not use best</option>
                <option value="doBest">Use best</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_mapped_reads" type="boolean" checked="False" label="Same the bowtie alignments to the non-coding RNA" />
    <param name="save_mapping_stats" type="boolean" checked="True" 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">
      <filter>save_mapped_reads is True</filter>
      <actions>
        <conditional name="refGenomeSource.genomeSource">
          <when value="indexed">
            <action type="metadata" name="dbkey">
              <option type="from_data_table" name="bowtie_rRNA_indexes" column="1" offset="0">
                <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                <filter type="param_value" ref="refGenomeSource.index" column="0"/>
              </option>
            </action>
          </when>

      </actions>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="genomeSource" value="history" />
      <param name="ownFile" value="chr9_100000bases.fa" />
      <param name="indexSettings" value="indexPreSet" />
      <param name="sPaired" value="single" />
      <param name="sInput1" ftype="fastqsanger" value="test.fastq" />
      <param name="alignMode" value="vMode" />
      <output name="output_unmapped_reads_l" ftype="fastqsanger" file="lesschr9.fastq" />
    </test>
    
  </tests>

  <help>

**What it does**