comparison bowtie_rRNA_removal_wrapper/bowtie_rRNA_removal_wrapper.xml @ 5:b300c15426f5 draft

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4:01ca7075c109

<tool id="bowtie_remove_rrna_wrapper" name="Remove rRNA using Bowtie" version="1.3">
  <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 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" />

                  <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" />
              </when>
            </conditional>
            <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">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>

              </when>
            </conditional> <!-- bestOption -->
            <conditional name="sAllValAlignsOption">
              <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)">
                <option value="noAllValAligns">Do not report all valid alignments</option>
                <option value="doAllValAligns">Report all valid alignments</option>
              </param>
              <when value="noAllValAligns">
                <param name="sValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per read (-k)" />
              </when>
              <when value="doAllValAligns" />
            </conditional>
            <param name="sSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m)" help="-1 for no limit" />
            <param name="sMaxFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)" />
            <param name="sUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" />
            <param name="sOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
            <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
          </when> <!-- full -->
        </conditional> <!-- sParams -->
      </when> <!-- single -->

            <param name="pTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
            <param name="pTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
            <conditional name="alignModeOption">
              <param name="alignMode" type="select" label="Alignment mode">
                <option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option>
                <option value="vMode">ignore qualities, limit end-to-end mismatches (-v)</option>
              </param>
              <when value="nMode">
                <param name="pMismatchSeed" type="integer" value="2" min="0" max="3" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
                <param name="pMismatchQual" type="integer" value="70" min="1" label="Maximum permitted total of quality values at all mismatched read positions (-e)" />
                <param name="pSeedLen" type="integer" value="28" min="5" label="Seed length (-l)" help="Minimum value is 5" />

                  <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" />
              </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">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>

              </when>
            </conditional>
            <conditional name="pAllValAlignsOption">
              <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)">
                <option value="noAllValAligns">Do not report all valid alignments</option>
                <option value="doAllValAligns">Report all valid alignments</option>
              </param>
              <when value="noAllValAligns">
                <param name="pValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per pair (-k)" />
              </when>
              <when value="doAllValAligns" />

            <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>

5:b300c15426f5

<tool id="bowtie_rRNA_removal_wrapper" name="Remove rRNA 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" />

                  <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="sSeedLen" type="integer" value="25" min="5" label="Seed length (-l)" help="Minimum value is 5" />
              </when>
            </conditional>
            <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>

              </when>
            </conditional> <!-- bestOption -->
            <conditional name="sAllValAlignsOption">
              <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)">
                <option value="noAllValAligns">Do not report all valid alignments</option>
                <option value="doAllValAligns" selected="true">Report all valid alignments</option>
              </param>
              <when value="noAllValAligns">
                <param name="sValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per read (-k)" />
              </when>
              <when value="doAllValAligns" />
            </conditional>
            <param name="sSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m)" help="-1 for no limit" />
            <param name="sMaxFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)" />
            <param name="sUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Write all reads that could not be aligned to a file (--un)" />
            <param name="sOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
            <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
          </when> <!-- full -->
        </conditional> <!-- sParams -->
      </when> <!-- single -->

            <param name="pTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
            <param name="pTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
            <conditional name="alignModeOption">
              <param name="alignMode" type="select" label="Alignment mode">
                <option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option>
                <option value="vMode" selected="true">ignore qualities, limit end-to-end mismatches (-v)</option>
              </param>
              <when value="nMode">
                <param name="pMismatchSeed" type="integer" value="2" min="0" max="3" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
                <param name="pMismatchQual" type="integer" value="70" min="1" label="Maximum permitted total of quality values at all mismatched read positions (-e)" />
                <param name="pSeedLen" type="integer" value="28" min="5" label="Seed length (-l)" help="Minimum value is 5" />

                  <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>

              </when>
            </conditional>
            <conditional name="pAllValAlignsOption">
              <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)">
                <option value="noAllValAligns">Do not report all valid alignments</option>
                <option value="doAllValAligns" selected="True">Report all valid alignments</option>
              </param>
              <when value="noAllValAligns">
                <param name="pValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per pair (-k)" />
              </when>
              <when value="doAllValAligns" />

            <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>