annotate tools/sr_mapping/bowtie_color_wrapper.xml @ 1:cdcb0ce84a1b

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<tool id="bowtie_color_wrapper" name="Map with Bowtie for SOLiD" version="1.1.2">
  <requirements><requirement type='package'>bowtie</requirement></requirements>
  <description></description>
  <command interpreter="python">
    bowtie_wrapper.py 
    ## Hackish setting of number of threads
    --threads="4"
    ## Outputs
      --output=$output
      #if str( $singlePaired.sPaired ) == "single"
        #if $output_unmapped_reads_l
          --output_unmapped_reads=$output_unmapped_reads_l
        #end if
        #if $output_suppressed_reads_l
          --output_suppressed_reads=$output_suppressed_reads_l
        #end if
      #else
        #if $output_unmapped_reads_l and $output_unmapped_reads_r
          --output_unmapped_reads_l=$output_unmapped_reads_l
          --output_unmapped_reads_r=$output_unmapped_reads_r
        #end if
        #if $output_suppressed_reads_l and $output_suppressed_reads_l
          --output_suppressed_reads_l=$output_suppressed_reads_l
          --output_suppressed_reads_r=$output_suppressed_reads_r
        #end if
      #end if
    ## Inputs
    --dataType="solid"
    --suppressHeader=$suppressHeader 
    --genomeSource=$refGenomeSource.genomeSource
    #if $refGenomeSource.genomeSource == "history":
      ##index already exists
      #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ):
        ##user previously built
        --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}"
        --do_not_build_index
      #else:
        ##build index on the fly
        --ref=$refGenomeSource.ownFile
        --indexSettings=$refGenomeSource.indexParams.indexSettings
        #if $refGenomeSource.indexParams.indexSettings == "indexFull":
          --iautoB=$refGenomeSource.indexParams.autoBehavior.autoB
          #if $refGenomeSource.indexParams.autoBehavior.autoB == "set":
            --ipacked=$refGenomeSource.indexParams.autoBehavior.packed
            --ibmax=$refGenomeSource.indexParams.autoBehavior.bmax
            --ibmaxdivn=$refGenomeSource.indexParams.autoBehavior.bmaxdivn
            --idcv=$refGenomeSource.indexParams.autoBehavior.dcv
          #end if
          --inodc=$refGenomeSource.indexParams.nodc
          --inoref=$refGenomeSource.indexParams.noref
          --ioffrate=$refGenomeSource.indexParams.offrate
          --iftab=$refGenomeSource.indexParams.ftab
          --intoa=$refGenomeSource.indexParams.ntoa
          --iendian=$refGenomeSource.indexParams.endian
          --iseed=$refGenomeSource.indexParams.seed
          --icutoff=$refGenomeSource.indexParams.cutoff
        #end if
      #end if
    #else
      ##use pre-built index
      --ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes_color' ].get_fields() )[0][-1] }"
    #end if
    --paired=$singlePaired.sPaired
    #if $singlePaired.sPaired == "single":
      --input1=$singlePaired.sInput1
      --params=$singlePaired.sParams.sSettingsType
      #if $singlePaired.sParams.sSettingsType == "full":
        --skip=$singlePaired.sParams.sSkip
        --alignLimit=$singlePaired.sParams.sAlignLimit
        --trimH=$singlePaired.sParams.sTrimH
        --trimL=$singlePaired.sParams.sTrimL
        --mismatchSeed=$singlePaired.sParams.sMismatchSeed
        --mismatchQual=$singlePaired.sParams.sMismatchQual
        --seedLen=$singlePaired.sParams.sSeedLen
        --rounding=$singlePaired.sParams.sRounding
        --maqSoapAlign=$singlePaired.sParams.sMaqSoapAlign
        --tryHard=$singlePaired.sParams.sTryHard
        --valAlign=$singlePaired.sParams.sValAlign
        --allValAligns=$singlePaired.sParams.sAllValAligns
        --suppressAlign=$singlePaired.sParams.sSuppressAlign
        --best=$singlePaired.sParams.sBestOption.sBest
        #if $singlePaired.sParams.sBestOption.sBest == "doBest":
          --maxBacktracks=$singlePaired.sParams.sBestOption.sdMaxBacktracks
          --strata=$singlePaired.sParams.sBestOption.sdStrata
        #else:
          --maxBacktracks=$singlePaired.sParams.sBestOption.snMaxBacktracks
        #end if
        --offrate=$singlePaired.sParams.sOffrate
        --seed=$singlePaired.sParams.sSeed
        --snpphred=$singlePaired.sParams.sSnpphred
        --snpfrac=$singlePaired.sParams.sSnpfrac
        --keepends=$singlePaired.sParams.sKeepends
      #end if
    #else:
      --input1=$singlePaired.pInput1
      --input2=$singlePaired.pInput2
      --maxInsert=$singlePaired.pMaxInsert
      --mateOrient=$singlePaired.pMateOrient
      --params=$singlePaired.pParams.pSettingsType
      #if $singlePaired.pParams.pSettingsType == "full":
        --skip=$singlePaired.pParams.pSkip
        --alignLimit=$singlePaired.pParams.pAlignLimit
        --trimH=$singlePaired.pParams.pTrimH
        --trimL=$singlePaired.pParams.pTrimL
        --mismatchSeed=$singlePaired.pParams.pMismatchSeed
        --mismatchQual=$singlePaired.pParams.pMismatchQual
        --seedLen=$singlePaired.pParams.pSeedLen
        --rounding=$singlePaired.pParams.pRounding
        --maqSoapAlign=$singlePaired.pParams.pMaqSoapAlign
        --minInsert=$singlePaired.pParams.pMinInsert
        --maxAlignAttempt=$singlePaired.pParams.pMaxAlignAttempt
        --forwardAlign=$singlePaired.pParams.pForwardAlign
        --reverseAlign=$singlePaired.pParams.pReverseAlign
        --tryHard=$singlePaired.pParams.pTryHard
        --valAlign=$singlePaired.pParams.pValAlign
        --allValAligns=$singlePaired.pParams.pAllValAligns
        --suppressAlign=$singlePaired.pParams.pSuppressAlign
        --best=$singlePaired.pParams.pBestOption.pBest
        #if $singlePaired.pParams.pBestOption.pBest == "doBest":
          --maxBacktracks=$singlePaired.pParams.pBestOption.pdMaxBacktracks
          --strata=$singlePaired.pParams.pBestOption.pdStrata
        #else:
          --maxBacktracks=$singlePaired.pParams.pBestOption.pnMaxBacktracks
        #end if
        --offrate=$singlePaired.pParams.pOffrate
        --seed=$singlePaired.pParams.pSeed
        --snpphred=$singlePaired.pParams.pSnpphred
        --snpfrac=$singlePaired.pParams.pSnpfrac
        --keepends=$singlePaired.pParams.pKeepends
      #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>
        <option value="history">Use one from the history</option>
      </param>
      <when value="indexed">
        <param name="index" type="select" label="Select the reference genome" help="if your genome of interest is not listed - contact Galaxy team">
          <options from_data_table="bowtie_indexes_color">
            <filter type="sort_by" column="2" />
            <validator type="no_options" message="No indexes are available" />
          </options>
        </param>
      </when>
      <when value="history">
        <param name="ownFile" type="data" format="bowtie_color_index,fasta" metadata_name="dbkey" label="Select the reference genome" />
        <conditional name="indexParams">
          <param name="indexSettings" type="select" label="Choose whether to use Default options for building indices or to Set your own" help="These settings are ignored when using a prebuilt index">
            <option value="indexPreSet">Default</option>
            <option value="indexFull">Set your own</option>
          </param>
          <when value="indexPreSet" />
          <when value="indexFull">
            <conditional name="autoBehavior">
              <param name="autoB" type="select" label="Choose to use automatic or specified behavior for some parameters (-a)" help="Allows you to set --packed, --bmax, --bmaxdivn, and --dcv">
                <option value="auto">Automatic behavior</option>
                <option value="set">Set values (sets --noauto and allows others to be set)</option>
              </param>
              <when value="auto" />
              <when value="set">
                <param name="packed" type="select" label="Whether or not to use a packed representation for DNA strings (--packed)">
                  <option value="unpacked">Use regular representation</option>
                  <option value="packed">Use packed representation</option>
                </param>
                <param name="bmax" type="integer" value="-1" label="Maximum number of suffixes allowed in a block (--bmax)" help="-1 for not specified. Must be at least 1" />
                <param name="bmaxdivn" type="integer" value="4" label="Maximum number of suffixes allowed in a block as a fraction of the length of the reference (--bmaxdivn)" />
                <param name="dcv" type="integer" value="1024" label="The period for the difference-cover sample (--dcv)" />
              </when>
            </conditional>
            <param name="nodc" type="select" label="Whether or not to disable the use of the difference-cover sample (--nodc)" help="Suffix sorting becomes quadratic-time in the worst case (with a very repetitive reference)">
              <option value="dc">Use difference-cover sample</option>
              <option value="nodc">Disable difference-cover sample</option>
            </param>
            <param name="noref" type="select" label="Whether or not to build the part of the reference index used only in paired-end alignment (-r)">
              <option value="ref">Build all index files</option>
              <option value="noref">Do not build paired-end alignment index files</option>
            </param>
            <param name="offrate" type="integer" value="5" label="How many rows get marked during annotation of some or all of the Burrows-Wheeler rows (-o)" />
            <param name="ftab" type="integer" value="10" label="The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query (-t)" help="ftab is 4^(n+1) bytes" />
            <param name="ntoa" type="select" label="Whether or not to convert Ns in the reference sequence to As (--ntoa)">
              <option value="no">Do not convert Ns</option>
              <option value="yes">Convert Ns to As</option>
            </param>
            <param name="endian" type="select" label="Endianness to use when serializing integers to the index file (--big/--little)" help="Little is most appropriate for Intel- and AMD-based architecture">
              <option value="little">Little</option>
              <option value="big">Big</option>
            </param> 
            <param name="seed" type="integer" value="-1" label="Seed for the pseudorandom number generator (--seed)" help="Use -1 to use default" />
            <param name="cutoff" type="integer" value="-1" label="Number of first bases of the reference sequence to index (--cutoff)" help="Use -1 to use default" />
          </when>  <!-- indexFull -->
        </conditional>  <!-- indexParams -->
      </when>  <!-- history -->
    </conditional>  <!-- refGenomeSource -->
    <conditional name="singlePaired">
      <param name="sPaired" type="select" label="Is this library mate-paired?">
        <option value="single">Single-end</option>
        <option value="paired">Paired-end</option>
      </param>
      <when value="single">
        <param name="sInput1" type="data" format="fastqcssanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
        <conditional name="sParams">
          <param name="sSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
            <option value="preSet">Commonly used</option>
            <option value="full">Full parameter list</option>
          </param>
          <when value="preSet" />
          <when value="full">
            <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" />  
            <param name="sAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" />  
            <param name="sTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
            <param name="sTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
            <param name="sMismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
            <param name="sMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" />
            <param name="sSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" />
            <param name="sRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)">
              <option value="round">Round to nearest 10</option>
              <option value="noRound">Do not round to nearest 10</option>
            </param>
            <param name="sMaqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" />
            <param name="sTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode">
              <option value="noTryHard">Do not try hard</option>
              <option value="doTryHard">Try hard</option>
            </param>
            <param name="sValAlign" type="integer" value="1" label="Report up to n valid alignments per read (-k)" />
            <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>
            <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)" />
            <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>
              </param>
              <when value="noBest">
                <param name="snMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
              </when>
              <when value="doBest">
                <param name="sdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
                <param name="sdStrata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)">
                  <option value="noStrata">Do not use strata option</option>
                  <option value="doStrata">Use strata option</option>
                </param>
              </when>
            </conditional> <!-- sBestOption -->
            <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" />
            <param name="sSnpphred" type="integer" value="-1" label="SNP penalty (ratio of SNPs per base in the subject genome) (--snpphred)" help="Enter this OR Ratio of SNPs per base" />
            <param name="sSnpfrac" type="float" value="0.001" label="Ratio of SNPs per base (estimated ratio for colorspace alignments) (--snpfrac)" help="Enter this OR SNP penalty" />
            <param name="sKeepends" type="select" label="Keep the extreme-ends nucleotides and qualities rather than trimming them (--col-keepends)">
              <option value="doKeepends">Keep ends</option>
              <option value="noKeepends">Trim ends</option>
            </param>
          </when> <!-- full -->
        </conditional> <!-- sParams -->
      </when> <!-- single -->
      <when value="paired">
        <param name="pInput1" type="data" format="fastqcssanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
        <param name="pInput2" type="data" format="fastqcssanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
        <param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" />
        <param name="pMateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)">
          <option value="ff">FF (for SOLiD)</option>
          <option value="fr">FR (for Illumina)</option>
          <option value="rf">RF</option>
        </param>
        <conditional name="pParams">
          <param name="pSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
            <option value="preSet">Commonly used</option>
            <option value="full">Full parameter list</option>
          </param>
          <when value="preSet" />
          <when value="full">
            <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" />  
            <param name="pAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" />  
            <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)" />
            <param name="pMismatchSeed" type="integer" value="2" 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" label="Maximum permitted total of quality values at mismatched read positions (-e)" />
            <param name="pSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" />
            <param name="pRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)">
              <option value="round">Round to nearest 10</option>
              <option value="noRound">Do not round to nearest 10</option>
            </param>
            <param name="pMaqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" />
            <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" />
            <param name="pMaxAlignAttempt" type="integer" value="100" label="Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate (--pairtries)" />
            <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align 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 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>
            <param name="pTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode">
              <option value="noTryHard">Do not try hard</option>
              <option value="doTryHard">Try hard</option>
            </param>
            <param name="pValAlign" type="integer" value="1" label="Report up to n valid arguments per pair (-k)" />
            <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>
            <param name="pSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a pair if more than n reportable alignments exist (-m)" help="-1 for no limit" />
            <param name="pMaxFile" 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="pUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" />
            <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>
              <when value="noBest">
                <param name="pnMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
              </when>
              <when value="doBest">
                <param name="pdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
                <param name="pdStrata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)">
                  <option value="noStrata">Do not use strata option</option>
                  <option value="doStrata">Use strata option</option>
                </param>
              </when>
            </conditional>  <!-- pBestOption -->
            <param name="pOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
            <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
            <param name="pSnpphred" type="integer" value="-1" label="SNP penalty (ratio of SNPs per base in the subject genome) (--snpphred)" help="Enter this OR Ratio of SNPs per base" />
            <param name="pSnpfrac" type="float" value="0.001" label="Ratio of SNPs per base (estimated ratio for colorspace alignments) (--snpfrac)" help="Enter this OR SNP penalty" />
            <param name="pKeepends" type="select" label="Keep the extreme-ends nucleotides and qualities rather than trimming them (--col-keepends)">
              <option value="doKeepends">Keep ends</option>
              <option value="noKeepends">Trim ends</option>
            </param>
          </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" help="Bowtie produces SAM with several lines of header information by default" />
  </inputs>
  <outputs>
    <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
      <actions>
        <conditional name="refGenomeSource.genomeSource">
          <when value="indexed">
            <action type="metadata" name="dbkey">
              <option type="from_data_table" name="bowtie_indexes_color" column="1" offset="0">
                <filter type="param_value" column="0" value="#" filter_by="startswith" keep="False"/>
                <filter type="param_value" ref="refGenomeSource.index" column="0"/>
              </option>
            </action>
          </when>
          <when value="history">
            <action type="metadata" name="dbkey">
              <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
            </action>
          </when>
        </conditional>
      </actions>
    </data>
    <data format="fastqcssanger" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
      <filter>((
          singlePaired['sPaired'] == "single" and
          singlePaired['sParams']['sSettingsType'] == "full" and
          singlePaired['sParams']['sMaxFile'] is True
        ) or (
          singlePaired['sPaired'] == "paired" and
          singlePaired['pParams']['pSettingsType'] == "full" and
          singlePaired['pParams']['pMaxFile'] is True
        ))
      </filter>
    </data>
    <data format="fastqcssanger" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
      <filter>singlePaired['sPaired'] == "paired"</filter>
      <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
      <filter>singlePaired['pParams']['pMaxFile'] is True</filter>
    </data>
    <data format="fastqcssanger" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
      <filter>
        ((
          singlePaired['sPaired'] == "single" and
          singlePaired['sParams']['sSettingsType'] == "full" and
          singlePaired['sParams']['sUnmappedFile'] is True
        ) or (
          singlePaired['sPaired'] == "paired" and
          singlePaired['pParams']['pSettingsType'] == "full" and
          singlePaired['pParams']['pUnmappedFile'] is True
        ))
      </filter>
    </data>
    <data format="fastqcssanger" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
      <filter>singlePaired['sPaired'] == "paired"</filter>
      <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
      <filter>singlePaired['pParams']['pUnmappedFile'] is True</filter>
    </data>
  </outputs>
  <tests>
    <test>
      <!--
      Bowtie command:
      bowtie -q -p 4 -S +sam-nohead -C chrM_color test-data/bowtie_in1.fastqcssanger > bowtie_out1_u.sam
      sort bowtie_out1_u.sam > bowtie_out1.sam
      -p is the number of threads, which is hardcoded above. You need to replace the + with 2 dashes. 
      chrM_color needs to be the base location/name of the index files.
      -->
      <param name="genomeSource" value="indexed" />
      <param name="index" value="equCab2chrM" />
      <param name="sPaired" value="single" />
      <param name="sInput1" ftype="fastqcssanger" value="bowtie_in1.fastqcssanger" />
      <param name="sSettingsType" value="preSet" />
      <param name="suppressHeader" value="true" />
      <output name="output" ftype="sam" file="bowtie_out1.sam" sort="True" />
    </test>
    <test>
      <!--
      Bowtie command:
      bowtie-build -C -f test-data/chr_m.fasta chrM_color
      bowtie -q -X 1000 +ff -p 4 -S +sam-nohead -C -n 2 -e 70 -l 28 -X 250 +pairtries 100 +maxbts 125 -k 1 +snpfrac 0.001 +col-keepends +un bowtie_out3_u.fastq chrM_color -1 test-data/bowtie_in3.fastqcssanger -2 test-data/bowtie_in4.fastqcssanger > bowtie_out2_u.sam
      sort bowtie_out2_u.sam > bowtie_out2.sam
      sort bowtie_out3_u_1.sam > bowtie_out3_1.sam
      sort bowtie_out3_u_2.sam > bowtie_out3_2.sam
      Then also need to modify bowtie_out3_1.sam and bowtie_out3_2.sam so that all @ lines come before sequence lines.
      The two unmapped output files will be named bowtie_out4_1.fastq and bowtie_out4_2.fastq
      -p is the number of threads, hardcoded above. 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="chr_m.fasta" />
      <param name="indexSettings" value="indexPreSet" />
      <param name="sPaired" value="paired" />
      <param name="pInput1" ftype="fastqcssanger" value="bowtie_in3.fastqcssanger" />
      <param name="pInput2" ftype="fastqcssanger" value="bowtie_in4.fastqcssanger" />
      <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="pMismatchSeed" value="2" />
      <param name="pMismatchQual" value="70" />
      <param name="pSeedLen" value="28" />
      <param name="pRounding" value="round" />
      <param name="pMaqSoapAlign" value="-1" />
      <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="noBest" />
      <param name="pnMaxBacktracks" value="125" />
      <param name="pOffrate" value="-1" />
      <param name="pSeed" value="-1" />
      <param name="pSnpphred" value="-1" />
      <param name="pSnpfrac" value="0.001" />
      <param name="pKeepends" value="doKeepends" />
      <param name="suppressHeader" value="true" />
      <output name="output" ftype="sam" file="bowtie_out2.sam" sort="True" />
      <output name="output_unmapped_reads_l" ftype="fastqcssanger" file="bowtie_out3_1.fastq" sort="True" />
      <output name="output_unmapped_reads_r" ftype="fastqcssanger" file="bowtie_out3_2.fastq" sort="True" />
    </test>
    <test>
      <!--
      Bowtie command:
      bowtie -q -p 4 -S +sam-nohead -C -n 2 -e 70 -l 28 +maxbts 125 -k 1 +snpfrac 0.001 +col-keepends chrM_color test-data/bowtie_in1.fastqcssanger > bowtie_out4_u.sam
      sort bowtie_out4_u.sam > bowtie_out4.sam
      -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes.
      chrM_base is the index files' location/base name. 
      -->
      <param name="genomeSource" value="indexed" />
      <param name="index" value="equCab2chrM" />
      <param name="sPaired" value="single" />
      <param name="sInput1" ftype="fastqcssanger" value="bowtie_in1.fastqcssanger" />
      <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="sMismatchSeed" value="2" />
      <param name="sMismatchQual" value="70" />
      <param name="sSeedLen" value="28" />
      <param name="sRounding" value="round" />
      <param name="sMaqSoapAlign" value="-1" />
      <param name="sTryHard" value="noTryHard" />
      <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="snMaxBacktracks" value="125" />
      <param name="sOffrate" value="-1" />
      <param name="sSeed" value="-1" />
      <param name="sSnpphred" value="-1" />
      <param name="sSnpfrac" value="0.001" />
      <param name="sKeepends" value="doKeepends" />
      <param name="suppressHeader" value="true" />
      <output name="output" ftype="sam" file="bowtie_out4.sam" sort="True" />
    </test>
    <test>
      <!--
      Bowtie command:
      bowtie-build +noauto +bmaxdivn 4 +dcv 1024 +offrate 5 +ftabchars 10 +little -C -f test-data/chr_m.fasta chrM_color
      bowtie -q -X 1000 +ff -p 4 -S +sam-nohead -C chrM_color -1 test-data/bowtie_in3.fastqcssanger -2 test-data/bowtie_in4.fastqcssanger > bowtie_out5_u.sam
      sort bowtie_out5_u.sam > bowtie_out5.sam
      -p is the number of threads, hardcoded above. 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="chr_m.fasta" />
      <param name="indexSettings" value="indexFull" />
      <param name="autoB" value="set" />
      <param name="packed" value="unpacked" />
      <param name="bmax" value="-1" />
      <param name="bmaxdivn" value="4" />
      <param name="dcv" value="1024" />
      <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="cutoff" value="-1" />
      <param name="sPaired" value="paired" />
      <param name="pInput1" ftype="fastqcssanger" value="bowtie_in3.fastqcssanger" />
      <param name="pInput2" ftype="fastqcssanger" value="bowtie_in4.fastqcssanger" />
      <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_out5.sam" sort="True" />
    </test>
  </tests> 

  <help>

**What it does**

Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.

.. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml

------

**Know what you are doing**

.. class:: warningmark

There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.

 .. __: http://bowtie-bio.sourceforge.net/index.shtml

------

**Input formats**

Bowtie accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files.

------

**A Note on Built-in Reference Genomes**

Some genomes have multiple variants. If only one "type" of genome is listed, it is the Full version, which means that everything that came in the original genome data download (possibly with mitochondrial and plasmid DNA added if it wasn't already included). The Full version is available for every genome. Some genomes also come in the Canonical variant, which contains only the "canonical" (well-defined) chromosomes or segments, such as chr1-chr22, chrX, chrY, and chrM for human. Other variations include gender. These will come in the canonical form only, so the general Canonical variant is actually Canonical Female and the other is Canonical Male (identical to female excluding chrX).

------

**Outputs**

The output is in SAM format, and has the following columns::

    Column  Description
  --------  --------------------------------------------------------
   1 QNAME  Query (pair) NAME
   2 FLAG   bitwise FLAG
   3 RNAME  Reference sequence NAME
   4 POS    1-based leftmost POSition/coordinate of clipped sequence
   5 MAPQ   MAPping Quality (Phred-scaled)
   6 CIGAR  extended CIGAR string
   7 MRNM   Mate Reference sequence NaMe ('=' if same as RNAME)
   8 MPOS   1-based Mate POSition
   9 ISIZE  Inferred insert SIZE
  10 SEQ    query SEQuence on the same strand as the reference
  11 QUAL   query QUALity (ASCII-33 gives the Phred base quality)
  12 OPT    variable OPTional fields in the format TAG:VTYPE:VALUE

The flags are as follows::

    Flag  Description
  ------  -------------------------------------
  0x0001  the read is paired in sequencing
  0x0002  the read is mapped in a proper pair
  0x0004  the query sequence itself is unmapped
  0x0008  the mate is unmapped
  0x0010  strand of the query (1 for reverse)
  0x0020  strand of the mate
  0x0040  the read is the first read in a pair
  0x0080  the read is the second read in a pair
  0x0100  the alignment is not primary

It looks like this (scroll sideways to see the entire example)::

  QNAME	FLAG	RNAME	POS	MAPQ	CIAGR	MRNM	MPOS	ISIZE	SEQ	QUAL	OPT
  HWI-EAS91_1_30788AAXX:1:1:1761:343	4	*	0	0	*	*	0	0	AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG	hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
  HWI-EAS91_1_30788AAXX:1:1:1578:331	4	*	0	0	*	*	0	0	GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG	hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh

-------

**Bowtie settings**

All of the options have a default value. You can change any of them. Most of the options in Bowtie have been implemented here.

------

**Bowtie parameter list**

This is an exhaustive list of Bowtie options:

For indexing (bowtie-build)::

  -a               No auto behavior. Disable the default behavior where bowtie automatically 
                   selects values for --bmax/--bmaxdivn/--dcv/--packed parameters according 
                   to the memory available. [off]
  --packed         Packing. Use a packed representation for DNA strings. [auto] 
  --bmax INT       Suffix maximum. The maximum number of suffixes allowed in a block. [auto]
  --bmaxdivn INT   Suffix maximum fraction. The maximum number of suffixes allowed in a block 
                   expressed as a fraction of the length of the reference. [4]
  --dcv INT        Difference-cover sample. Use INT as the period for the difference-cover 
                   sample. [1024]
  --nodc INT       No difference-cover sample. Disable the difference-cover sample. [off]
  -r               No reference indexes. Do not build the NAME.3.ebwt and NAME.4.ebwt portions 
                   of the index. Used only for paired-end alignment. [off]
  -o               Offrate. How many Burrows-Wheeler rows get marked by the indexer. The 
                   indexer will mark every 2^INT rows. The marked rows correspond to rows on 
                   the genome. [5]
  -t INT           Ftab. The lookup table used to calculate an initial Burrows-Wheeler range 
                   with respect to the first INT characters of the query. Ftab is 4^INT+1 
                   bytes. [10]
  --ntoa           N conversion. Convert Ns to As before building the index. Otherwise, Ns are 
                   simply excluded from the index and Bowtie will not find alignments that 
                   overlap them. [off]
  --big            Endianness. Endianness to use when serializing integers to the index file. [off]
  --little         Endianness. [--little]
  --seed INT       Random seed. Use INT as the seed for the pseudo-random number generator. [off]
  --cutoff INT     Cutoff. Index only the first INT bases of the reference sequences (cumulative 
                   across sequences) and ignore the rest. [off]

For aligning (bowtie)::

  -s INT           Skip. Do not align the first INT reads or pairs in the input. [off]
  -u INT           Align limit. Only align the first INT reads/pairs from the input. [no limit]
  -5 INT           High-quality trim. Trim INT bases from the high-quality (left) end of each 
                   read before alignment. [0]
  -3 INT           Low-quality trim. Trim INT bases from the low-quality (right) end of each 
                   read before alignment. [0]
  -n INT           Mismatch seed. Maximum number of mismatches permitted in the seed (defined 
                   with seed length option). Can be 0, 1, 2, or 3. [2]
  -e INT           Mismatch quality. Maximum permitted total of quality values at mismatched 
                   read positions. Bowtie rounds quality values to the nearest 10 and saturates 
                   at 30. [70]
  -l INT           Seed length. The number of bases on the high-quality end of the read to 
                   which the -n ceiling applies. Must be at least 5. [28]
  --nomaqround     Suppress MAQ rounding. Values are internally rounded to the nearest 10 and 
                   saturate at 30. This options turns off that rounding. [off] 
  -v INT           MAQ- or SOAP-like alignment policy. This option turns off the default 
                   MAQ-like alignment policy in favor of a SOAP-like one. End-to-end alignments 
                   with at most INT mismatches. [off]
  -I INT           Minimum insert. The minimum insert size for valid paired-end alignments. 
                   Does checking on untrimmed reads if -5 or -3 is used. [0]
  -X INT           Maximum insert. The maximum insert size for valid paired-end alignments. 
                   Does checking on untrimmed reads if -5 or -3 is used. [250]
  --fr             Mate orientation. The upstream/downstream mate orientations for a valid 
                   paired-end alignment against the forward reference strand. [--fr]
  --rf             Mate orientation. [off]
  --ff             Mate orientation. [off]
  --pairtries INT  Maximum alignment attempts for paired-end data. [100] 
  --nofw           No forward aligning. Choosing this option means that Bowtie will not attempt 
                   to align against the forward reference strand. [off]
  --norc           No reverse-complement aligning. Setting this will mean that Bowtie will not 
                   attempt to align against the reverse-complement reference strand. [off]
  --maxbts INT     Maximum backtracks. The maximum number of backtracks permitted when aligning 
                   a read in -n 2 or -n 3 mode. [125 without --best] [800 with --best]
  -y               Try hard. Try as hard as possible to find valid alignments when they exist, 
                   including paired-end alignments. [off]
  --chunkmbs INT   Thread memory. The number of megabytes of memory a given thread is given to 
                   store path descriptors in --best mode. [32]
  -k INT           Valid alignments. The number of valid alignments per read or pair. [off] 
  -a               All valid alignments. Choosing this means that all valid alignments per read 
                   or pair will be reported. [off]
  -m INT           Suppress alignments. Suppress all alignments for a particular read or pair 
                   if more than INT reportable alignments exist for it. [no limit]
  --best           Best mode. Make Bowtie guarantee that reported singleton alignments are 
                   "best" in terms of stratum (the number of mismatches) and quality values at 
                   mismatched position. [off]
  --strata         Best strata. When running in best mode, report alignments that fall into the 
                   best stratum if there are ones falling into more than one. [off]
  -o INT           Offrate override. Override the offrate of the index with INT. Some row 
                   markings are discarded when index read into memory. INT must be greater than 
                   the value used to build the index (default: 5). [off]
  --seed INT       Random seed. Use INT as the seed for the pseudo-random number generator. [off]
  --snpphred INT   Use INT as the SNP penalty for decoding colorspace alignments. True ratio of 
                   SNPs per base in the subject genome. [see --snpfrac]
  --snpfrac DEC    Use DEC as the estimated ratio of SNPs per base when decoding colorspace 
                   alignments. [0.001]
  --col-keepends   Keep the extreme-end nucleotides and qualities when decoding colorspace 
                   alignments. [off]

  </help>
</tool>