bowtie_wrappers: bowtie_wrapper.xml comparison

comparison bowtie_wrapper.xml @ 4:df86f29bedee draft

planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty

author	devteam
date	Tue, 21 Jul 2015 13:04:45 -0400
parents	42c4463baaad
children	306077e393d4

comparison

equal deleted inserted replaced

-:9ca609a2a421
+:df86f29bedee
-<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.2">
+<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.3">
 <requirements>
-<requirement type='package' version="0.12.7">bowtie</requirement>
+<requirement type="package" version="0.12.7">bowtie</requirement>
 </requirements>
 <description></description>
-<parallelism method="basic"></parallelism>
+<version_command>bowtie --version</version_command>
 <command interpreter="python">
 bowtie_wrapper.py
 ## Set number of threads
 --threads="\${GALAXY_SLOTS:-4}"
 ## Outputs
 --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="${refGenomeSource.index.fields.path}"
 #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}"
+#if $singlePaired.sParams.alignModeOption.alignMode == 'nMode'
---mismatchQual="${singlePaired.sParams.sMismatchQual}"
+--mismatchSeed="${singlePaired.sParams.alignModeOption.sMismatchSeed}"
---seedLen="${singlePaired.sParams.sSeedLen}"
+--mismatchQual="${singlePaired.sParams.alignModeOption.sMismatchQual}"
---rounding="${singlePaired.sParams.sRounding}"
+--seedLen="${singlePaired.sParams.alignModeOption.sSeedLen}"
---maqSoapAlign="${singlePaired.sParams.sMaqSoapAlign}"
+--rounding="${singlePaired.sParams.alignModeOption.sRounding}"
---tryHard="${singlePaired.sParams.sTryHard}"
+#else
---valAlign="${singlePaired.sParams.sValAlign}"
+--maxMismatches="${singlePaired.sParams.alignModeOption.maxMismatches}"
---allValAligns="${singlePaired.sParams.sAllValAligns}"
+#end if
+--forwardAlign="${singlePaired.sParams.sForwardAlign}"
+--reverseAlign="${singlePaired.sParams.sReverseAlign}"
+--tryHard="${singlePaired.sParams.sBestOption.sTryHardOption.sTryHard}"
+--allValAligns="${singlePaired.sParams.sAllValAlignsOption.sAllValAligns}"
+#if $singlePaired.sParams.sAllValAlignsOption.sAllValAligns == "noAllValAligns"
+--valAlign="${singlePaired.sParams.sAllValAlignsOption.sValAlign}"
+#end if
 --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}"
+#if $singlePaired.sParams.sBestOption.sTryHardOption.sTryHard == "noTryHard"
+--maxBacktracks="${singlePaired.sParams.sBestOption.sTryHardOption.sdMaxBacktracks}"
+#end if
 #else:
---maxBacktracks="${singlePaired.sParams.sBestOption.snMaxBacktracks}"
+#if $singlePaired.sParams.sBestOption.sTryHardOption.sTryHard == "noTryHard"
+--maxBacktracks="${singlePaired.sParams.sBestOption.sTryHardOption.snMaxBacktracks}"
+#end if
 #end if
 --offrate="${singlePaired.sParams.sOffrate}"
 --seed="${singlePaired.sParams.sSeed}"
 #end if
 #else:
 #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}"
+#if $singlePaired.pParams.alignModeOption.alignMode == 'nMode'
---mismatchQual="${singlePaired.pParams.pMismatchQual}"
+--mismatchSeed="${singlePaired.pParams.alignModeOption.pMismatchSeed}"
---seedLen="${singlePaired.pParams.pSeedLen}"
+--mismatchQual="${singlePaired.pParams.alignModeOption.pMismatchQual}"
---rounding="${singlePaired.pParams.pRounding}"
+--seedLen="${singlePaired.pParams.alignModeOption.pSeedLen}"
---maqSoapAlign="${singlePaired.pParams.pMaqSoapAlign}"
+--rounding="${singlePaired.pParams.alignModeOption.pRounding}"
+#else
+--maxMismatches="${singlePaired.pParams.alignModeOption.maxMismatches}"
+#end if
 --minInsert="${singlePaired.pParams.pMinInsert}"
---maxAlignAttempt="${singlePaired.pParams.pMaxAlignAttempt}"
 --forwardAlign="${singlePaired.pParams.pForwardAlign}"
 --reverseAlign="${singlePaired.pParams.pReverseAlign}"
---tryHard="${singlePaired.pParams.pTryHard}"
+--tryHard="${singlePaired.pParams.pBestOption.pTryHardOption.pTryHard}"
---valAlign="${singlePaired.pParams.pValAlign}"
+--allValAligns="${singlePaired.pParams.pAllValAlignsOption.pAllValAligns}"
---allValAligns="${singlePaired.pParams.pAllValAligns}"
+#if $singlePaired.pParams.pAllValAlignsOption.pAllValAligns == "noAllValAligns"
+--valAlign="${singlePaired.pParams.pAllValAlignsOption.pValAlign}"
+#end if
 --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}"
+#if $singlePaired.pParams.pBestOption.pTryHardOption.pTryHard == "noTryHard"
+--maxAlignAttempt="${singlePaired.pParams.pBestOption.pTryHardOption.pMaxAlignAttempt}"
+--maxBacktracks="${singlePaired.pParams.pBestOption.pTryHardOption.pdMaxBacktracks}"
+#end if
 #else:
---maxBacktracks="${singlePaired.pParams.pBestOption.pnMaxBacktracks}"
+#if $singlePaired.pParams.pBestOption.pTryHardOption.pTryHard == "noTryHard"
+--maxAlignAttempt="${singlePaired.pParams.pBestOption.pTryHardOption.pMaxAlignAttempt}"
+--maxBacktracks="${singlePaired.pParams.pBestOption.pTryHardOption.pnMaxBacktracks}"
+#end if
 #end if
 --offrate="${singlePaired.pParams.pOffrate}"
 --seed="${singlePaired.pParams.pSeed}"
 #end if
 #end if
 <param name="ownFile" type="data" format="bowtie_base_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)">
+<param name="packed" type="select" label="Whether or not to use a packed representation for DNA strings (--packed)" help="Packed representation saves memory but makes indexing 2-3 times slower">
 <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)" />
+<param name="dcv" type="integer" value="1024" min="3" label="The period for the difference-cover sample (--dcv)" help="A larger period yields less memory overhead, but may make suffix sorting slower, especially if repeats are present" />
 </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="offrate" type="integer" value="5" min="0" label="The indexer will mark every 2^n Burrows-Wheeler rows with their corresponding location on the genome (-o)" help="Marking more rows makes reference-position lookups faster, but requires more memory to hold the annotations at runtime" />
-<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="ftab" type="integer" value="10" min="1" label="The size of the ftab lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query (-t)" help="ftab size 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="sInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/>
 <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" />
+<conditional name="alignModeOption">
-<param name="sMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" />
+<param name="alignMode" type="select" label="Alignment mode">
-<param name="sSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" />
+<option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option>
-<param name="sRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)">
+<option value="vMode">ignore qualities, limit end-to-end mismatches (-v)</option>
-<option value="round">Round to nearest 10</option>
+</param>
-<option value="noRound">Do not round to nearest 10</option>
+<when value="nMode">
+<param name="sMismatchSeed" 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="sMismatchQual" type="integer" value="70" min="1" label="Maximum permitted total of quality values at all mismatched read positions (-e)" />
+<param name="sSeedLen" type="integer" value="28" min="5" 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)" help="Maq accepts quality values in the Phred quality scale, but internally rounds values to the nearest 10, with a maximum of 30. By default, bowtie also rounds this way">
+<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" />
+</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="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="sReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
-<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="reverse">Align against the reverse-complement reference strand</option>
-<option value="noTryHard">Do not try hard</option>
+<option value="noReverse">Do not align against the reverse-complement reference strand</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)" />
+<conditional name="sTryHardOption">
+<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>
+<when value="noTryHard">
+<param name="snMaxBacktracks" type="integer" value="125" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
+</when>
+<when value="doTryHard" />
+</conditional>
 </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>
+<conditional name="sTryHardOption">
+<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>
+<when value="noTryHard">
+<param name="sdMaxBacktracks" type="integer" value="800" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
+</when>
+<when value="doTryHard" />
+</conditional>
 </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="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
 <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file">
 <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">>
 <column name="name" index="0"/>
 <column name="value" index="0"/>
 <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/>
 </options>
 </param>
 <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="fr">FR (for Illumina)</option>
 <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" />
+<conditional name="alignModeOption">
-<param name="pMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" />
+<param name="alignMode" type="select" label="Alignment mode">
-<param name="pSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" />
+<option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option>
-<param name="pRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)">
+<option value="vMode">ignore qualities, limit end-to-end mismatches (-v)</option>
-<option value="round">Round to nearest 10</option>
+</param>
-<option value="noRound">Do not round to nearest 10</option>
+<when value="nMode">
-</param>
+<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="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="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" />
+<param name="pRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)" help="Maq accepts quality values in the Phred quality scale, but internally rounds values to the nearest 10, with a maximum of 30. By default, bowtie also rounds this way">
+<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" />
+</when>
+</conditional>
 <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 against the forward reference strand (--nofw)">
-<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)">
+<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>
-<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)" />
+<conditional name="pTryHardOption">
+<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>
+<when value="noTryHard">
+<param name="pMaxAlignAttempt" type="integer" value="100" min="1" 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="pnMaxBacktracks" type="integer" value="125" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
+</when>
+<when value="doTryHard" />
+</conditional>
 </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>
+<conditional name="pTryHardOption">
+<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>
+<when value="noTryHard">
+<param name="pMaxAlignAttempt" type="integer" value="100" min="1" 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="pdMaxBacktracks" type="integer" value="800" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
+</when>
+<when value="doTryHard" />
+</conditional>
 </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" />
+</conditional>
+<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)" />
 <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" />
 </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" />
+<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">
 <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" />
 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="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="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="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="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="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="fastqillumna" file="bowtie_out8_1.fastqillumina.sorted" 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="fastqillumna" file="bowtie_out8_2.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="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="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="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 +maxbts 125 -y -k 1 chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out9_u.sam
+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="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="sMaqSoapAlign" value="-1" />
+<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="snMaxBacktracks" value="125" />
 <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>
 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="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="fastqsanger" value="bowtie_in5.fastqsanger" />
 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
 <param name="pMaxInsert" value="1000" />
 <param name="pMateOrient" value="ff" />
 **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)
 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
 -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
+-t INT             The ftab 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
+with respect to the first INT characters of the query. Ftab size 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]
 -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
+--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
+-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
+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]
 --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>
+<citations>
+<citation type="doi">10.1186/gb-2009-10-3-r25</citation>
+</citations>
 </tool>

Mercurial > repos > devteam > bowtie_wrappers

comparison bowtie_wrapper.xml @ 4:df86f29bedee draft