details: http://www.bx.psu.edu/hg/galaxy/rev/4fc2b29d6393
changeset: 3236:4fc2b29d6393
user: Greg Von Kuster <greg(a)bx.psu.edu>
date: Wed Jan 13 18:33:42 2010 -0500
description:
Bug fix for uploading files to a history.
diffstat:
lib/galaxy/tools/actions/upload_common.py | 10 +++++-----
1 files changed, 5 insertions(+), 5 deletions(-)
diffs (32 lines):
diff -r bfb0f6c64093 -r 4fc2b29d6393 lib/galaxy/tools/actions/upload_common.py
--- a/lib/galaxy/tools/actions/upload_common.py Wed Jan 13 18:02:37 2010 -0500
+++ b/lib/galaxy/tools/actions/upload_common.py Wed Jan 13 18:33:42 2010 -0500
@@ -59,7 +59,7 @@
role = trans.sa_session.query( trans.app.model.Role ).get( role_id )
library_bunch.roles.append( role )
return library_bunch
-def get_precreated_datasets( trans, params, data_obj, controller='root' ):
+def get_precreated_datasets( trans, params, data_obj, controller='root' ):
"""
Get any precreated datasets (when using asynchronous uploads).
"""
@@ -75,15 +75,15 @@
log.exception( 'Unable to load precreated dataset (%s) sent in upload form' % id )
continue
if data_obj is trans.app.model.HistoryDatasetAssociation:
- if user is None and trans.galaxy_session.current_history != data.history:
+ if trans.user is None and trans.galaxy_session.current_history != data.history:
log.error( 'Got a precreated dataset (%s) but it does not belong to anonymous user\'s current session (%s)' % ( data.id, trans.galaxy_session.id ) )
- elif data.history.user != user:
- log.error( 'Got a precreated dataset (%s) but it does not belong to current user (%s)' % ( data.id, user.id ) )
+ elif data.history.user != trans.user:
+ log.error( 'Got a precreated dataset (%s) but it does not belong to current user (%s)' % ( data.id, trans.user.id ) )
else:
rval.append( data )
elif data_obj is trans.app.model.LibraryDatasetDatasetAssociation:
if controller == 'library' and not trans.app.security_agent.can_add_library_item( roles, data.library_dataset.folder ):
- log.error( 'Got a precreated dataset (%s) but this user (%s) is not allowed to write to it' % ( data.id, user.id ) )
+ log.error( 'Got a precreated dataset (%s) but this user (%s) is not allowed to write to it' % ( data.id, trans.user.id ) )
else:
rval.append( data )
return rval
details: http://www.bx.psu.edu/hg/galaxy/rev/35d2a31cfbaf
changeset: 3230:35d2a31cfbaf
user: Kelly Vincent <kpvincent(a)bx.psu.edu>
date: Tue Jan 12 16:49:02 2010 -0500
description:
Changed the bowtie wrapper tool into two different tools: one for illumina data and one for solid
diffstat:
test-data/bowtie_in1.fastq | 5 -
test-data/bowtie_in2.fastq | 4 -
test-data/bowtie_in3.fastq | 4 -
test-data/bowtie_in4.fastqsanger | 2 +-
test-data/bowtie_out3.sam | 4 +-
test-data/bowtie_out7.sam | 4 +-
tool_conf.xml.sample | 1 +
tools/sr_mapping/bowtie_color_wrapper.xml | 659 +++++++++++++
tools/sr_mapping/bowtie_wrapper.py | 51 +-
tools/sr_mapping/bowtie_wrapper.xml | 1423 +++++++++-------------------
tools/sr_mapping/bowtie_wrapper_code.py | 13 +-
11 files changed, 1141 insertions(+), 1029 deletions(-)
diffs (2385 lines):
diff -r b78de785df21 -r 35d2a31cfbaf test-data/bowtie_in1.fastq
--- a/test-data/bowtie_in1.fastq Tue Jan 12 15:48:21 2010 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-@HWI-EAS91_1_30788AAXX:1:1:1513:715/1
-GTTTTTTNNGCATAGATGTTTAGTTGTGGTAGTCAG
-+/1
-IIIIIII""IIIIIIIIIIIIIIIIIIIDI?II-+I
-
diff -r b78de785df21 -r 35d2a31cfbaf test-data/bowtie_in2.fastq
--- a/test-data/bowtie_in2.fastq Tue Jan 12 15:48:21 2010 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-@HWI-EAS91_1_30788AAXX:1:2:618:346/1
-TAGACTACGAAAGTGACTTTAATACCTCTGACTACA
-+
-IIIIIIIIIIIIIIIIIIIIIIIIIIIII%4II;I3
diff -r b78de785df21 -r 35d2a31cfbaf test-data/bowtie_in3.fastq
--- a/test-data/bowtie_in3.fastq Tue Jan 12 15:48:21 2010 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-@HWI-EAS91_1_30788AAXX:1:2:618:346/2
-ATAGGCTGAATTAGCAATGGATGGTGGGGTTTATCG
-+
-IIIIIIIIIIIIIII9I.II5II6DFIIIIII*I2)
diff -r b78de785df21 -r 35d2a31cfbaf test-data/bowtie_in4.fastqsanger
--- a/test-data/bowtie_in4.fastqsanger Tue Jan 12 15:48:21 2010 -0500
+++ b/test-data/bowtie_in4.fastqsanger Tue Jan 12 16:49:02 2010 -0500
@@ -1,4 +1,4 @@
@869_1532_1255/2
-2200333112212110002221031T
+T1301222000112122113330022
+
;89<:==5<8>69;8=<9;<>9:=<
diff -r b78de785df21 -r 35d2a31cfbaf test-data/bowtie_out3.sam
--- a/test-data/bowtie_out3.sam Tue Jan 12 15:48:21 2010 -0500
+++ b/test-data/bowtie_out3.sam Tue Jan 12 16:49:02 2010 -0500
@@ -1,2 +1,2 @@
-869_1532_1255 163 chrM 3727 255 27M = 3752 50 GGAAATATGTCTGACAAAAGAGTTACT !!PTUVYQPSUSNSRTXTSVYVRVX<! XA:i:2 MD:Z:27 NM:i:0 CM:i:2
-869_1532_1255 83 chrM 3752 255 25M = 3727 -50 CTTTGATAGAGTAAAACATAGAGGC >USVY_UOXZWRQRSUY[\^XQR!! XA:i:1 MD:Z:25 NM:i:0 CM:i:1
+869_1532_1255 179 chrM 3727 255 25M = 3752 50 GGAAATATGTCTGACAAAAGAGTTA !!RVYVSTXTRSNSUSPQYVUTPR; XA:i:1 MD:Z:25 NM:i:0 CM:i:1
+869_1532_1255 115 chrM 3752 255 25M = 3727 -50 CTTTGATAGAGTAAAACATAGAGGC >USVY_UOXZWRQRSUY[\^XQR!! XA:i:1 MD:Z:25 NM:i:0 CM:i:1
diff -r b78de785df21 -r 35d2a31cfbaf test-data/bowtie_out7.sam
--- a/test-data/bowtie_out7.sam Tue Jan 12 15:48:21 2010 -0500
+++ b/test-data/bowtie_out7.sam Tue Jan 12 16:49:02 2010 -0500
@@ -1,2 +1,2 @@
-869_1532_1255 163 chrM 3728 255 25M = 3752 47 GAAATATGTCTGACAAAAGAGTTAC !PTUVYQPSUSNSRTXTSVYVRVX< XA:i:2 MD:Z:25 NM:i:0 CM:i:2
-869_1532_1255 83 chrM 3753 255 23M = 3727 -49 TTTGATAGAGTAAAACATAGAGG USVY_UOXZWRQRSUY[\^XQR! XA:i:1 MD:Z:23 NM:i:0 CM:i:1
+869_1532_1255 77 * 0 0 * * 0 0 CAGGGTTCCAAATCGGGTTGCAAG =;8:?@=?;;9:8;=>;5A?;<8> XM:i:0
+869_1532_1255 141 * 0 0 * * 0 0 TACGGGAAACCGCGGCCTTTAAGG ;89<:==5<8>69;8=<9;<>9:= XM:i:0
diff -r b78de785df21 -r 35d2a31cfbaf tool_conf.xml.sample
--- a/tool_conf.xml.sample Tue Jan 12 15:48:21 2010 -0500
+++ b/tool_conf.xml.sample Tue Jan 12 16:49:02 2010 -0500
@@ -192,6 +192,7 @@
<section name="NGS: Mapping" id="solexa_tools">
<tool file="sr_mapping/lastz_wrapper.xml" />
<tool file="sr_mapping/bowtie_wrapper.xml" />
+ <tool file="sr_mapping/bowtie_color_wrapper.xml" />
<tool file="sr_mapping/bwa_wrapper.xml" />
<tool file="metag_tools/megablast_wrapper.xml" />
<tool file="metag_tools/megablast_xml_parser.xml" />
diff -r b78de785df21 -r 35d2a31cfbaf tools/sr_mapping/bowtie_color_wrapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/sr_mapping/bowtie_color_wrapper.xml Tue Jan 12 16:49:02 2010 -0500
@@ -0,0 +1,659 @@
+<tool id="bowtie_color_wrapper" name="Map with Bowtie for SOLiD" version="1.0.0">
+ <description></description>
+ <command interpreter="python">
+ bowtie_wrapper.py
+ --threads="4"
+ --dataType="solid"
+ --output=$output
+ --suppressHeader=$suppressHeader
+ --genomeSource=$refGenomeSource.genomeSource
+ #if $refGenomeSource.genomeSource == "history":
+ --ref=$refGenomeSource.ownFile
+ --dbkey=$dbkey
+ --indexSettings=$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=$refGenomeSource.indexParams.autoBehavior.dcv
+ #else:
+ --ipacked="None"
+ --ibmax="None"
+ --ibmaxdivn="None"
+ --idcv="None"
+ #end if
+ --inodc=$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=$refGenomeSource.indexParams.cutoff
+ #else:
+ --iautoB="None"
+ --ipacked="None"
+ --ibmax="None"
+ --ibmaxdivn="None"
+ --idcv="None"
+ --inodc="None"
+ --inoref="None"
+ --ioffrate="None"
+ --iftab="None"
+ --intoa="None"
+ --iendian="None"
+ --iseed="None"
+ --icutoff="None"
+ #end if
+ #else:
+ --ref=$refGenomeSource.index.value
+ --dbkey="None"
+ --indexSettings="None"
+ --iautoB="None"
+ --ipacked="None"
+ --ibmax="None"
+ --ibmaxdivn="None"
+ --idcv="None"
+ --inodc="None"
+ --inoref="None"
+ --ioffrate="None"
+ --iftab="None"
+ --intoa="None"
+ --iendian="None"
+ --iseed="None"
+ --icutoff="None"
+ #end if
+ --paired=$singlePaired.sPaired
+ #if $singlePaired.sPaired == "single":
+ --input1=$singlePaired.sInput1
+ --input2="None"
+ --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
+ --strata="None"
+ #end if
+ --offrate=$singlePaired.sParams.sOffrate
+ --seed=$singlePaired.sParams.sSeed
+ --snpphred=$singlePaired.sParams.sSnpphred
+ --snpfrac=$singlePaired.sParams.sSnpfrac
+ --keepends=$singlePaired.sParams.sKeepends
+ #else:
+ --skip="None"
+ --alignLimit="None"
+ --trimH="None"
+ --trimL="None"
+ --mismatchSeed="None"
+ --mismatchQual="None"
+ --seedLen="None"
+ --rounding="None"
+ --maqSoapAlign="None"
+ --tryHard="None"
+ --valAlign="None"
+ --allValAligns="None"
+ --suppressAlign="None"
+ --best="None"
+ --maxBacktracks="None"
+ --strata="None"
+ --offrate="None"
+ --seed="None"
+ --snpphred="None"
+ --snpfrac="None"
+ --keepends="None"
+ #end if
+ --minInsert="None"
+ --maxInsert="None"
+ --mateOrient="None"
+ --maxAlignAttempt="None"
+ --forwardAlign="None"
+ --reverseAlign="None"
+ #else:
+ --input1=$singlePaired.pInput1
+ --input2=$singlePaired.pInput2
+ --params=$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=$singlePaired.pParams.pMinInsert
+ --maxInsert=$singlePaired.pParams.pMaxInsert
+ --mateOrient=$singlePaired.pParams.pMateOrient
+ --maxAlignAttempt=$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
+ --strata="None"
+ #end if
+ --offrate=$singlePaired.pParams.pOffrate
+ --seed=$singlePaired.pParams.pSeed
+ --snpphred=$singlePaired.pParams.pSnpphred
+ --snpfrac=$singlePaired.pParams.pSnpfrac
+ --keepends=$singlePaired.pParams.pKeepends
+ #else:
+ --skip="None"
+ --alignLimit="None"
+ --trimH="None"
+ --trimL="None"
+ --mismatchSeed="None"
+ --mismatchQual="None"
+ --seedLen="None"
+ --rounding="None"
+ --maqSoapAlign="None"
+ --minInsert="None"
+ --maxInsert="None"
+ --mateOrient="None"
+ --maxAlignAttempt="None"
+ --forwardAlign="None"
+ --reverseAlign="None"
+ --tryHard="None"
+ --valAlign="None"
+ --allValAligns="None"
+ --suppressAlign="None"
+ --best="None"
+ --maxBacktracks="None"
+ --strata="None"
+ --offrate="None"
+ --seed="None"
+ --snpphred="None"
+ --snpfrac="None"
+ --keepends="None"
+ #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_file="bowtie_indices_color.loc">
+ <column name="value" index="1" />
+ <column name="name" index="0" />
+ </options>
+ </param>
+ </when>
+ <when value="history">
+ <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a 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">
+ <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 (-p)">
+ <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 (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> <!-- cIndexFull -->
+ </conditional> <!-- cIndexParams -->
+ </when> <!-- cHistory -->
+ </conditional> <!-- cRefGenomeSource -->
+ <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="fastqsanger" 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 arguments 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" />
+ <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> <!-- csBestOption -->
+ <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 (--keepends)">
+ <option value="doKeepends">Keep ends</option>
+ <option value="noKeepends">Trim ends</option>
+ </param>
+ </when> <!-- csFull -->
+ </conditional> <!-- csParams -->
+ </when> <!-- cSingle -->
+ <when value="paired">
+ <param name="pInput1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
+ <param name="pInput2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
+ <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="pMaxInsert" type="integer" value="250" 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>
+ <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" />
+ <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> <!-- cpBestOption -->
+ <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 (--keepends)">
+ <option value="doKeepends">Keep ends</option>
+ <option value="noKeepends">Trim ends</option>
+ </param>
+ </when> <!-- cpFull -->
+ </conditional> <!-- cpParams -->
+ </when> <!-- cPaired -->
+ </conditional> <!-- cSinglePaired -->
+ <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information" />
+ </inputs>
+ <outputs>
+ <data format="sam" name="output" />
+ </outputs>
+ <tests>
+ <test>
+ <!--
+ Bowtie command:
+ bowtie -p 4 -S +sam-nohead -q -C chrM_color test-data/bowtie_in1.fastqsanger > test-data/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="fastqsanger" value="bowtie_in1.fastqsanger" />
+ <param name="sSettingsType" value="preSet" />
+ <param name="suppressHeader" value="true" />
+ <output name="output" ftype="sam" file="bowtie_out1.sam" />
+ </test>
+ <test>
+ <!--
+ Bowtie command:
+ bowtie-build -f -C test-data/chr_m.fasta chrM_color
+ bowtie -n 2 -e 70 -l 28 -X 250 +ff +pairtries 100 +maxbts 125 -k 1 -C +snpfrac 0.001 +col-keepends -p 4 -S +sam-nohead -q chrM_color -1 test-data/bowtie_in3.fastqsanger -2 test-data/bowtie_in4.fastqsanger > test-data/bowtie_out3.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="indexPreSet" />
+ <param name="sPaired" value="paired" />
+ <param name="pInput1" ftype="fastqsanger" value="bowtie_in3.fastqsanger" />
+ <param name="pInput2" ftype="fastqsanger" value="bowtie_in4.fastqsanger" />
+ <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="pMaxInsert" value="250" />
+ <param name="pMateOrient" value="ff" />
+ <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="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_out3.sam" />
+ </test>
+ <test>
+ <!--
+ Bowtie command:
+ bowtie -n 2 -e 70 -l 28 +maxbts 125 -k 1 -C +snpfrac 0.001 +col-keepends -p 4 -S +sam-nohead -q chrM_color test-data/bowtie_in1.fastqsanger > test-data/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="indexed" />
+ <param name="index" value="equCab2chrM" />
+ <param name="sPaired" value="single" />
+ <param name="sInput1" ftype="fastqsanger" value="bowtie_in1.fastqsanger" />
+ <param name="sSettingsType" value="full" />
+ <param name="sSkip" value="0" />
+ <param name="sAlignLimit" value="-1" />
+ <param name="sTrimH" value="0" />
+ <param name="sTrimL" value="0" />
+ <param name="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="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_out5.sam" />
+ </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 -p 4 -S +sam-nohead -q -C chrM_color -1 test-data/bowtie_in3.fastqsanger -2 test-data/bowtie_in4.fastqsanger > test-data/bowtie_out7.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="cHistory" />
+ <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="fastqsanger" value="bowtie_in3.fastqsanger" />
+ <param name="pInput2" ftype="fastqsanger" value="bowtie_in4.fastqsanger" />
+ <param name="pSettingsType" value="preSet" />
+ <param name="suppressHeader" value="true" />
+ <output name="output" ftype="sam" file="bowtie_out7.sam" />
+ </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 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 `documentation`__ and experimenting. Fortunaly, Galaxy makes experimenting easy.
+
+ .. __: http://bowtie-bio.sourceforge.net/index.shtml
+
+------
+
+**Input formats**
+
+Bowtie accepts files in Sanger FASTQ format.
+
+------
+
+**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/--dcv/--packed parameters according to the memory available. [off]
+ -p 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]
+ --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]
+ -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]
+ --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>
+ <code file="bowtie_wrapper_code.py" />
+</tool>
diff -r b78de785df21 -r 35d2a31cfbaf tools/sr_mapping/bowtie_wrapper.py
--- a/tools/sr_mapping/bowtie_wrapper.py Tue Jan 12 15:48:21 2010 -0500
+++ b/tools/sr_mapping/bowtie_wrapper.py Tue Jan 12 16:49:02 2010 -0500
@@ -42,7 +42,7 @@
-S, --seed=S: Seed for pseudo-random number generator
-d, --dbkey=d: Dbkey of reference genome
-C, --params=C: Whether to use default or specified parameters
- -u, --iauto_b=u: Automatic or specified behavior
+ -u, --iautoB=u: Automatic or specified behavior
-K, --ipacked=K: Whether or not to use a packed representation for DNA strings
-Q, --ibmax=Q: Maximum number of suffixes allowed in a block
-Y, --ibmaxdivn=Y: Maximum number of suffixes allowed in a block as a fraction of the length of the reference
@@ -105,7 +105,7 @@
parser.add_option( '-7', '--keepends', dest='keepends', help='Keep extreme-end nucleotides and qualities' )
parser.add_option( '-d', '--dbkey', dest='dbkey', help='Dbkey of reference genome' )
parser.add_option( '-C', '--params', dest='params', help='Whether to use default or specified parameters' )
- parser.add_option( '-u', '--iauto_b', dest='iauto_b', help='Automatic or specified behavior' )
+ parser.add_option( '-u', '--iautoB', dest='iautoB', help='Automatic or specified behavior' )
parser.add_option( '-K', '--ipacked', dest='ipacked', help='Whether or not to use a packed representation for DNA strings' )
parser.add_option( '-Q', '--ibmax', dest='ibmax', help='Maximum number of suffixes allowed in a block' )
parser.add_option( '-Y', '--ibmaxdivn', dest='ibmaxdivn', help='Maximum number of suffixes allowed in a block as a fraction of the length of the reference' )
@@ -129,17 +129,17 @@
else:
colorspace = ''
# index if necessary
- if options.genomeSource == 'cHistory' or options.genomeSource == 'xHistory':
+ if options.genomeSource == 'history':
# set up commands
- if options.index_settings =='cIndexPreSet' or options.index_settings == 'xIndexPreSet':
+ if options.index_settings =='indexPreSet':
indexing_cmds = '%s' % colorspace
else:
try:
- if options.iauto_b == 'set':
- iauto_b = '--noauto'
+ if options.iautoB != 'None' and options.iautoB == 'set':
+ iautoB = '--noauto'
else:
- iauto_b = ''
- if options.ipacked == 'packed':
+ iautoB = ''
+ if options. ipacked != 'None' and options.ipacked == 'packed':
ipacked = '--packed'
else:
ipacked = ''
@@ -155,11 +155,11 @@
idcv = '--dcv %s' % options.idcv
else:
idcv = ''
- if options.inodc == 'nodc':
+ if options.inodc != 'None' and options.inodc == 'nodc':
inodc = '--nodc'
else:
inodc = ''
- if options.inoref == 'noref':
+ if options.inoref != 'None' and options.inoref == 'noref':
inoref = '--noref'
else:
inoref = ''
@@ -167,24 +167,24 @@
iftab = '--ftabchars %s' % options.iftab
else:
iftab = ''
- if options.intoa == 'yes':
+ if options.intoa != 'None' and options.intoa == 'yes':
intoa = '--ntoa'
else:
intoa = ''
- if options.iendian == 'big':
+ if options.iendian != 'None' and options.iendian == 'big':
iendian = '--big'
else:
iendian = '--little'
- if int( options.iseed ) > 0:
+ if options.iseed != 'None' and int( options.iseed ) > 0:
iseed = '--seed %s' % options.iseed
else:
iseed = ''
- if int( options.icutoff ) > 0:
+ if options.icutoff != 'None' and int( options.icutoff ) > 0:
icutoff = '--cutoff %s' % options.icutoff
else:
icutoff = ''
indexing_cmds = '%s %s %s %s %s %s %s --offrate %s %s %s %s %s %s %s' % \
- ( iauto_b, ipacked, ibmax, ibmaxdivn, idcv, inodc,
+ ( iautoB, ipacked, ibmax, ibmaxdivn, idcv, inodc,
inoref, options.ioffrate, iftab, intoa, iendian,
iseed, icutoff, colorspace )
except ValueError:
@@ -206,8 +206,7 @@
suppressHeader = '--sam-nohead'
else:
suppressHeader = ''
- if options.params == 'csPreSet' or options.params == 'cpPreSet' or \
- options.params == 'xsPreSet' or options.params == 'xpPreSet':
+ if options.params == 'preSet':
aligning_cmds = '-p %s -S %s -q %s ' % ( options.threads, suppressHeader, colorspace )
else:
try:
@@ -215,27 +214,28 @@
skip = '-s %s' % options.skip
else:
skip = ''
- if int( options.alignLimit ) >= 0:
+ if options.alignLimit != 'None' and int( options.alignLimit ) >= 0:
alignLimit = '-u %s' % options.alignLimit
else:
alignLimit = ''
- if int( options.trimH ) > 0:
+ if options.trimH != 'None' and int( options.trimH ) > 0:
trimH = '-5 %s' % options.trimH
else:
trimH = ''
- if int( options.trimL ) > 0:
+ if options.trimL != 'None' and int( options.trimL ) > 0:
trimL = '-3 %s' % options.trimL
else:
trimL = ''
- if options.mismatchSeed == '0' or options.mismatchSeed == '1' or options.mismatchSeed == '2' or options.mismatchSeed == '3':
+ if options. mismatchSeed != 'None' and (options.mismatchSeed == '0' or options.mismatchSeed == '1' \
+ or options.mismatchSeed == '2' or options.mismatchSeed == '3'):
mismatchSeed = '-n %s' % options.mismatchSeed
else:
mismatchSeed = ''
- if int( options.mismatchQual ) >= 0:
+ if options.mismatchQual != 'None' and int( options.mismatchQual ) >= 0:
mismatchQual = '-e %s' % options.mismatchQual
else:
mismatchQual = ''
- if int( options.seedLen ) >= 5:
+ if options.seedLen != 'None' and int( options.seedLen ) >= 5:
seedLen = '-l %s' % options.seedLen
else:
seedLen = ''
@@ -292,8 +292,7 @@
suppressAlign = '-m %s' % options.suppressAlign
else:
suppressAlign = ''
- if options.best == 'csDoBest' or options.best == 'cpDoBest' or \
- options.best == 'xsDoBest' or options.best == 'xpDoBest':
+ if options.best == 'doBest':
best = '--best'
else:
best = ''
@@ -332,7 +331,7 @@
except ValueError, e:
stop_err( 'Something is wrong with the alignment parameters and the alignment could not be run\n' + str( e ) )
# prepare actual aligning commands
- if options.paired == 'cPaired' or options.paired == 'xPaired':
+ if options.paired == 'paired':
cmd2 = 'bowtie %s %s -1 %s -2 %s > %s 2> /dev/null' % ( aligning_cmds, options.ref, options.input1, options.input2, options.output )
else:
cmd2 = 'bowtie %s %s %s > %s 2> /dev/null' % ( aligning_cmds, options.ref, options.input1, options.output )
diff -r b78de785df21 -r 35d2a31cfbaf tools/sr_mapping/bowtie_wrapper.xml
--- a/tools/sr_mapping/bowtie_wrapper.xml Tue Jan 12 15:48:21 2010 -0500
+++ b/tools/sr_mapping/bowtie_wrapper.xml Tue Jan 12 16:49:02 2010 -0500
@@ -1,780 +1,383 @@
-<tool id="bowtie_wrapper" name="Map with Bowtie" version="1.0.5">
+<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.0.6">
<description></description>
<command interpreter="python">
- bowtie_wrapper.py --threads="4" --output=$output --suppressHeader=$suppressHeader --dataType=$solidOrSolexa.dataType
-#if $solidOrSolexa.dataType == "solid":
- --genomeSource=$solidOrSolexa.cRefGenomeSource.cGenomeSource
- #if $solidOrSolexa.cRefGenomeSource.cGenomeSource == "cIndexed":
- --ref=$solidOrSolexa.cRefGenomeSource.cIndex.value
- --dbkey="None"
- --indexSettings="None"
- --iauto_b="None"
- --ipacked="None"
- --ibmax="None"
- --ibmaxdivn="None"
- --idcv="None"
- --inodc="None"
- --inoref="None"
- --ioffrate="None"
- --iftab="None"
- --intoa="None"
- --iendian="None"
- --iseed="None"
- --icutoff="None"
- #else:
- --ref=$solidOrSolexa.cRefGenomeSource.cOwnFile
- --dbkey=$dbkey
- --indexSettings=$solidOrSolexa.cRefGenomeSource.cIndexParams.cIndexSettings
- #if $solidOrSolexa.cRefGenomeSource.cIndexParams.cIndexSettings == "cIndexFull":
- --iauto_b=$solidOrSolexa.cRefGenomeSource.cIndexParams.cAutoBehavior.cAutoB == "cSet"
- #if $solidOrSolexa.cRefGenomeSource.cIndexParams.cAutoBehavior.cAutoB == "cSet":
- --ipacked=$solidOrSolexa.cRefGenomeSource.cIndexParams.cAutoBehavior.cPacked
- --ibmax=$solidOrSolexa.cRefGenomeSource.cIndexParams.cAutoBehavior.cBmax
- --ibmaxdivn=$solidOrSolexa.cRefGenomeSource.cIndexParams.cAutoBehavior.cBmaxdivn
- --idcv=$solidOrSolexa.cRefGenomeSource.cIndexParams.cAutoBehavior.cDcv
- #else:
- --ipacked="None"
- --ibmax="None"
- --ibmaxdivn="None"
- --idcv="None"
- #end if
- --inodc=$solidOrSolexa.cRefGenomeSource.cIndexParams.cNodc
- --inoref=$solidOrSolexa.cRefGenomeSource.cIndexParams.cNoref
- --ioffrate=$solidOrSolexa.cRefGenomeSource.cIndexParams.cOffrate
- --iftab=$solidOrSolexa.cRefGenomeSource.cIndexParams.cFtab
- --intoa=$solidOrSolexa.cRefGenomeSource.cIndexParams.cNtoa
- --iendian=$solidOrSolexa.cRefGenomeSource.cIndexParams.cEndian
- --iseed=$solidOrSolexa.cRefGenomeSource.cIndexParams.cSeed
- --icutoff=$solidOrSolexa.cRefGenomeSource.cIndexParams.cCutoff
- #else:
- --iauto_b="None"
- --ipacked="None"
- --ibmax="None"
- --ibmaxdivn="None"
- --idcv="None"
- --inodc="None"
- --inoref="None"
- --ioffrate="None"
- --iftab="None"
- --intoa="None"
- --iendian="None"
- --iseed="None"
- --icutoff="None"
- #end if
- #end if
- --paired=$solidOrSolexa.cSinglePaired.cSPaired
- #if $solidOrSolexa.cSinglePaired.cSPaired == "cSingle":
- --input1=$solidOrSolexa.cSinglePaired.csInput1
- --input2="None"
- --params=$solidOrSolexa.cSinglePaired.csParams.csSettingsType
- #if $solidOrSolexa.cSinglePaired.csParams.csSettingsType == "csFull":
- --skip=$solidOrSolexa.cSinglePaired.csParams.csSkip
- --alignLimit=$solidOrSolexa.cSinglePaired.csParams.csAlignLimit
- --trimH=$solidOrSolexa.cSinglePaired.csParams.csTrimH
- --trimL=$solidOrSolexa.cSinglePaired.csParams.csTrimL
- --mismatchSeed=$solidOrSolexa.cSinglePaired.csParams.csMismatchSeed
- --mismatchQual=$solidOrSolexa.cSinglePaired.csParams.csMismatchQual
- --seedLen=$solidOrSolexa.cSinglePaired.csParams.csSeedLen
- --rounding=$solidOrSolexa.cSinglePaired.csParams.csRounding
- --maqSoapAlign=$solidOrSolexa.cSinglePaired.csParams.csMaqSoapAlign
- --tryHard=$solidOrSolexa.cSinglePaired.csParams.csTryHard
- --valAlign=$solidOrSolexa.cSinglePaired.csParams.csValAlign
- --allValAligns=$solidOrSolexa.cSinglePaired.csParams.csAllValAligns
- --suppressAlign=$solidOrSolexa.cSinglePaired.csParams.csSuppressAlign
- --best=$solidOrSolexa.cSinglePaired.csParams.csBestOption.csBest
- #if $solidOrSolexa.cSinglePaired.csParams.csBestOption.csBest == "csDoBest":
- --maxBacktracks=$solidOrSolexa.cSinglePaired.csParams.csBestOption.csdMaxBacktracks
- --strata=$solidOrSolexa.cSinglePaired.csParams.csBestOption.csdStrata
- #else:
- --maxBacktracks=$solidOrSolexa.cSinglePaired.csParams.csBestOption.csnMaxBacktracks
- --strata="None"
- #end if
- --offrate=$solidOrSolexa.cSinglePaired.csParams.csOffrate
- --seed=$solidOrSolexa.cSinglePaired.csParams.csSeed
- --snpphred=$solidOrSolexa.cSinglePaired.csParams.csSnpphred
- --snpfrac=$solidOrSolexa.cSinglePaired.csParams.csSnpfrac
- --keepends=$solidOrSolexa.cSinglePaired.csParams.csKeepends
- #else:
- --skip="None"
- --alignLimit="None"
- --trimH="None"
- --trimL="None"
- --mismatchSeed="None"
- --mismatchQual="None"
- --seedLen="None"
- --rounding="None"
- --maqSoapAlign="None"
- --tryHard="None"
- --valAlign="None"
- --allValAligns="None"
- --suppressAlign="None"
- --best="None"
- --maxBacktracks="None"
- --strata="None"
- --offrate="None"
- --seed="None"
- --snpphred="None"
- --snpfrac="None"
- --keepends="None"
- #end if
- --minInsert="None"
- --maxInsert="None"
- --mateOrient="None"
- --maxAlignAttempt="None"
- --forwardAlign="None"
- --reverseAlign="None"
- #else:
- --input1=$solidOrSolexa.cSinglePaired.cpInput1
- --input2=$solidOrSolexa.cSinglePaired.cpInput2
- --params=$solidOrSolexa.cSinglePaired.cpParams.cpSettingsType
- #if $solidOrSolexa.cSinglePaired.cpParams.cpSettingsType == "cpFull":
- --skip=$solidOrSolexa.cSinglePaired.cpParams.cpSkip
- --alignLimit=$solidOrSolexa.cSinglePaired.cpParams.cpAlignLimit
- --trimH=$solidOrSolexa.cSinglePaired.cpParams.cpTrimH
- --trimL=$solidOrSolexa.cSinglePaired.cpParams.cpTrimL
- --mismatchSeed=$solidOrSolexa.cSinglePaired.cpParams.cpMismatchSeed
- --mismatchQual=$solidOrSolexa.cSinglePaired.cpParams.cpMismatchQual
- --seedLen=$solidOrSolexa.cSinglePaired.cpParams.cpSeedLen
- --rounding=$solidOrSolexa.cSinglePaired.cpParams.cpRounding
- --maqSoapAlign=$solidOrSolexa.cSinglePaired.cpParams.cpMaqSoapAlign
- --minInsert=$solidOrSolexa.cSinglePaired.cpParams.cpMinInsert
- --maxInsert=$solidOrSolexa.cSinglePaired.cpParams.cpMaxInsert
- --mateOrient=$solidOrSolexa.cSinglePaired.cpParams.cpMateOrient
- --maxAlignAttempt=$solidOrSolexa.cSinglePaired.cpParams.cpMaxAlignAttempt
- --forwardAlign=$solidOrSolexa.cSinglePaired.cpParams.cpForwardAlign
- --reverseAlign=$solidOrSolexa.cSinglePaired.cpParams.cpReverseAlign
- --tryHard=$solidOrSolexa.cSinglePaired.cpParams.cpTryHard
- --valAlign=$solidOrSolexa.cSinglePaired.cpParams.cpValAlign
- --allValAligns=$solidOrSolexa.cSinglePaired.cpParams.cpAllValAligns
- --suppressAlign=$solidOrSolexa.cSinglePaired.cpParams.cpSuppressAlign
- --best=$solidOrSolexa.cSinglePaired.cpParams.cpBestOption.cpBest
- #if $solidOrSolexa.cSinglePaired.cpParams.cpBestOption.cpBest == "cpDoBest":
- --maxBacktracks=$solidOrSolexa.cSinglePaired.cpParams.cpBestOption.cpdMaxBacktracks
- --strata=$solidOrSolexa.cSinglePaired.cpParams.cpBestOption.cpdStrata
- #else:
- --maxBacktracks=$solidOrSolexa.cSinglePaired.cpParams.cpBestOption.cpnMaxBacktracks
- --strata="None"
- #end if
- --offrate=$solidOrSolexa.cSinglePaired.cpParams.cpOffrate
- --seed=$solidOrSolexa.cSinglePaired.cpParams.cpSeed
- --snpphred=$solidOrSolexa.cSinglePaired.cpParams.cpSnpphred
- --snpfrac=$solidOrSolexa.cSinglePaired.cpParams.cpSnpfrac
- --keepends=$solidOrSolexa.cSinglePaired.cpParams.cpKeepends
- #else:
- --skip="None"
- --alignLimit="None"
- --trimH="None"
- --trimL="None"
- --mismatchSeed="None"
- --mismatchQual="None"
- --seedLen="None"
- --rounding="None"
- --maqSoapAlign="None"
- --tryHard="None"
- --valAlign="None"
- --allValAligns="None"
- --suppressAlign="None"
- --best="None"
- --maxBacktracks="None"
- --strata="None"
- --offrate="None"
- --seed="None"
- --snpphred="None"
- --snpfrac="None"
- --keepends="None"
- --minInsert="None"
- --maxInsert="None"
- --mateOrient="None"
- --maxAlignAttempt="None"
- --forwardAlign="None"
- --reverseAlign="None"
- #end if
- #end if
-#else:
- --genomeSource=$solidOrSolexa.xRefGenomeSource.xGenomeSource
- #if $solidOrSolexa.xRefGenomeSource.xGenomeSource == "xIndexed":
- --ref=$solidOrSolexa.xRefGenomeSource.xIndex.value
- --dbkey="None"
- --indexSettings="None"
- --iauto_b="None"
- --ipacked="None"
- --ibmax="None"
- --ibmaxdivn="None"
- --idcv="None"
- --inodc="None"
- --inoref="None"
- --ioffrate="None"
- --iftab="None"
- --intoa="None"
- --iendian="None"
- --iseed="None"
- --icutoff="None"
- #else:
- --ref=$solidOrSolexa.xRefGenomeSource.xOwnFile
- --dbkey=$dbkey
- --indexSettings=$solidOrSolexa.xRefGenomeSource.xIndexParams.xIndexSettings
- #if $solidOrSolexa.xRefGenomeSource.xIndexParams.xIndexSettings == "xIndexFull":
- --iauto_b=$solidOrSolexa.xRefGenomeSource.xIndexParams.xAutoBehavior.xAutoB == "xSet"
- #if $solidOrSolexa.xRefGenomeSource.xIndexParams.xAutoBehavior.xAutoB == "xSet":
- --ipacked=$solidOrSolexa.xRefGenomeSource.xIndexParams.xAutoBehavior.xPacked
- --ibmax=$solidOrSolexa.xRefGenomeSource.xIndexParams.xAutoBehavior.xBmax
- --ibmaxdivn=$solidOrSolexa.xRefGenomeSource.xIndexParams.xAutoBehavior.xBmaxdivn
- --idcv=$solidOrSolexa.xRefGenomeSource.xIndexParams.xAutoBehavior.xDcv
- #else:
- --ipacked="None"
- --ibmax="None"
- --ibmaxdivn="None"
- --idcv="None"
- #end if
- --inodc=$solidOrSolexa.xRefGenomeSource.xIndexParams.xNodc
- --inoref=$solidOrSolexa.xRefGenomeSource.xIndexParams.xNoref
- --ioffrate=$solidOrSolexa.xRefGenomeSource.xIndexParams.xOffrate
- --iftab=$solidOrSolexa.xRefGenomeSource.xIndexParams.xFtab
- --intoa=$solidOrSolexa.xRefGenomeSource.xIndexParams.xNtoa
- --iendian=$solidOrSolexa.xRefGenomeSource.xIndexParams.xEndian
- --iseed=$solidOrSolexa.xRefGenomeSource.xIndexParams.xSeed
- --icutoff=$solidOrSolexa.xRefGenomeSource.xIndexParams.xCutoff
- #else:
- --iauto_b="None"
- --ipacked="None"
- --ibmax="None"
- --ibmaxdivn="None"
- --idcv="None"
- --inodc="None"
- --inoref="None"
- --ioffrate="None"
- --iftab="None"
- --intoa="None"
- --iendian="None"
- --iseed="None"
- --icutoff="None"
- #end if
- #end if
- --paired=$solidOrSolexa.xSinglePaired.xSPaired
- #if $solidOrSolexa.xSinglePaired.xSPaired == "xSingle":
- --input1=$solidOrSolexa.xSinglePaired.xsInput1
- --input2="None"
- --params=$solidOrSolexa.xSinglePaired.xsParams.xsSettingsType
- #if $solidOrSolexa.xSinglePaired.xsParams.xsSettingsType == "xsFull":
- --skip=$solidOrSolexa.xSinglePaired.xsParams.xsSkip
- --alignLimit=$solidOrSolexa.xSinglePaired.xsParams.xsAlignLimit
- --trimH=$solidOrSolexa.xSinglePaired.xsParams.xsTrimH
- --trimL=$solidOrSolexa.xSinglePaired.xsParams.xsTrimL
- --mismatchSeed=$solidOrSolexa.xSinglePaired.xsParams.xsMismatchSeed
- --mismatchQual=$solidOrSolexa.xSinglePaired.xsParams.xsMismatchQual
- --seedLen=$solidOrSolexa.xSinglePaired.xsParams.xsSeedLen
- --rounding=$solidOrSolexa.xSinglePaired.xsParams.xsRounding
- --maqSoapAlign=$solidOrSolexa.xSinglePaired.xsParams.xsMaqSoapAlign
- --tryHard=$solidOrSolexa.xSinglePaired.xsParams.xsTryHard
- --valAlign=$solidOrSolexa.xSinglePaired.xsParams.xsValAlign
- --allValAligns=$solidOrSolexa.xSinglePaired.xsParams.xsAllValAligns
- --suppressAlign=$solidOrSolexa.xSinglePaired.xsParams.xsSuppressAlign
- --best=$solidOrSolexa.xSinglePaired.xsParams.xsBestOption.xsBest
- #if $solidOrSolexa.xSinglePaired.xsParams.xsBestOption.xsBest == "xsDoBest":
- --maxBacktracks=$solidOrSolexa.xSinglePaired.xsParams.xsBestOption.xsdMaxBacktracks
- --strata=$solidOrSolexa.xSinglePaired.xsParams.xsBestOption.xsdStrata
- #else:
- --maxBacktracks=$solidOrSolexa.xSinglePaired.xsParams.xsBestOption.xsnMaxBacktracks
- --strata="None"
- #end if
- --offrate=$solidOrSolexa.xSinglePaired.xsParams.xsOffrate
- --seed=$solidOrSolexa.xSinglePaired.xsParams.xsSeed
- #else:
- --skip="None"
- --alignLimit="None"
- --trimH="None"
- --trimL="None"
- --mismatchSeed="None"
- --mismatchQual="None"
- --seedLen="None"
- --rounding="None"
- --maqSoapAlign="None"
- --tryHard="None"
- --valAlign="None"
- --allValAligns="None"
- --suppressAlign="None"
- --best="None"
- --maxBacktracks="None"
- --strata="None"
- --offrate="None"
- --seed="None"
- #end if
- --snpphred="None"
- --snpfrac="None"
- --keepends="None"
- --minInsert="None"
- --maxInsert="None"
- --mateOrient="None"
- --maxAlignAttempt="None"
- --forwardAlign="None"
- --reverseAlign="None"
- #else:
- --input1=$solidOrSolexa.xSinglePaired.xpInput1
- --input2=$solidOrSolexa.xSinglePaired.xpInput2
- --params=$solidOrSolexa.xSinglePaired.xpParams.xpSettingsType
- #if $solidOrSolexa.xSinglePaired.xpParams.xpSettingsType == "xpFull":
- --skip=$solidOrSolexa.xSinglePaired.xpParams.xpSkip
- --alignLimit=$solidOrSolexa.xSinglePaired.xpParams.xpAlignLimit
- --trimH=$solidOrSolexa.xSinglePaired.xpParams.xpTrimH
- --trimL=$solidOrSolexa.xSinglePaired.xpParams.xpTrimL
- --mismatchSeed=$solidOrSolexa.xSinglePaired.xpParams.xpMismatchSeed
- --mismatchQual=$solidOrSolexa.xSinglePaired.xpParams.xpMismatchQual
- --seedLen=$solidOrSolexa.xSinglePaired.xpParams.xpSeedLen
- --rounding=$solidOrSolexa.xSinglePaired.xpParams.xpRounding
- --maqSoapAlign=$solidOrSolexa.xSinglePaired.xpParams.xpMaqSoapAlign
- --minInsert=$solidOrSolexa.xSinglePaired.xpParams.xpMinInsert
- --maxInsert=$solidOrSolexa.xSinglePaired.xpParams.xpMaxInsert
- --mateOrient=$solidOrSolexa.xSinglePaired.xpParams.xpMateOrient
- --maxAlignAttempt=$solidOrSolexa.xSinglePaired.xpParams.xpMaxAlignAttempt
- --forwardAlign=$solidOrSolexa.xSinglePaired.xpParams.xpForwardAlign
- --reverseAlign=$solidOrSolexa.xSinglePaired.xpParams.xpReverseAlign
- --tryHard=$solidOrSolexa.xSinglePaired.xpParams.xpTryHard
- --valAlign=$solidOrSolexa.xSinglePaired.xpParams.xpValAlign
- --allValAligns=$solidOrSolexa.xSinglePaired.xpParams.xpAllValAligns
- --suppressAlign=$solidOrSolexa.xSinglePaired.xpParams.xpSuppressAlign
- --best=$solidOrSolexa.xSinglePaired.xpParams.xpBestOption.xpBest
- #if $solidOrSolexa.xSinglePaired.xpParams.xpBestOption.xpBest == "xpDoBest":
- --maxBacktracks=$solidOrSolexa.xSinglePaired.xpParams.xpBestOption.xpdMaxBacktracks
- --strata=$solidOrSolexa.xSinglePaired.xpParams.xpBestOption.xpdStrata
- #else:
- --maxBacktracks=$solidOrSolexa.xSinglePaired.xpParams.xpBestOption.xpnMaxBacktracks
- --strata="None"
- #end if
- --offrate=$solidOrSolexa.xSinglePaired.xpParams.xpOffrate
- --seed=$solidOrSolexa.xSinglePaired.xpParams.xpSeed
- #else:
- --skip="None"
- --alignLimit="None"
- --trimH="None"
- --trimL="None"
- --mismatchSeed="None"
- --mismatchQual="None"
- --seedLen="None"
- --rounding="None"
- --maqSoapAlign="None"
- --tryHard="None"
- --valAlign="None"
- --allValAligns="None"
- --suppressAlign="None"
- --best="None"
- --maxBacktracks="None"
- --strata="None"
- --offrate="None"
- --seed="None"
- --minInsert="None"
- --maxInsert="None"
- --mateOrient="None"
- --maxAlignAttempt="None"
- --forwardAlign="None"
- --reverseAlign="None"
- #end if
- --snpphred="None"
- --snpfrac="None"
- --keepends="None"
- #end if
-#end if
+ bowtie_wrapper.py
+ --threads="4"
+ --dataType="solexa"
+ --output=$output
+ --suppressHeader=$suppressHeader
+ --genomeSource=$refGenomeSource.genomeSource
+ --snpphred="None"
+ --snpfrac="None"
+ --keepends="None"
+ #if $refGenomeSource.genomeSource == "history":
+ --ref=$refGenomeSource.ownFile
+ --dbkey=$dbkey
+ --indexSettings=$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=$refGenomeSource.indexParams.autoBehavior.dcv
+ #else:
+ --ipacked="None"
+ --ibmax="None"
+ --ibmaxdivn="None"
+ --idcv="None"
+ #end if
+ --inodc=$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=$refGenomeSource.indexParams.cutoff
+ #else:
+ --iautoB="None"
+ --ipacked="None"
+ --ibmax="None"
+ --ibmaxdivn="None"
+ --idcv="None"
+ --inodc="None"
+ --inoref="None"
+ --ioffrate="None"
+ --iftab="None"
+ --intoa="None"
+ --iendian="None"
+ --iseed="None"
+ --icutoff="None"
+ #end if
+ #else:
+ --ref=$refGenomeSource.index.value
+ --dbkey="None"
+ --indexSettings="None"
+ --iautoB="None"
+ --ipacked="None"
+ --ibmax="None"
+ --ibmaxdivn="None"
+ --idcv="None"
+ --inodc="None"
+ --inoref="None"
+ --ioffrate="None"
+ --iftab="None"
+ --intoa="None"
+ --iendian="None"
+ --iseed="None"
+ --icutoff="None"
+ #end if
+ --paired=$singlePaired.sPaired
+ #if $singlePaired.sPaired == "single":
+ --input1=$singlePaired.sInput1
+ --input2="None"
+ --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
+ --strata="None"
+ #end if
+ --offrate=$singlePaired.sParams.sOffrate
+ --seed=$singlePaired.sParams.sSeed
+ #else:
+ --skip="None"
+ --alignLimit="None"
+ --trimH="None"
+ --trimL="None"
+ --mismatchSeed="None"
+ --mismatchQual="None"
+ --seedLen="None"
+ --rounding="None"
+ --maqSoapAlign="None"
+ --tryHard="None"
+ --valAlign="None"
+ --allValAligns="None"
+ --suppressAlign="None"
+ --best="None"
+ --maxBacktracks="None"
+ --strata="None"
+ --offrate="None"
+ --seed="None"
+ --snpphred="None"
+ --snpfrac="None"
+ --keepends="None"
+ #end if
+ --minInsert="None"
+ --maxInsert="None"
+ --mateOrient="None"
+ --maxAlignAttempt="None"
+ --forwardAlign="None"
+ --reverseAlign="None"
+ #else:
+ --input1=$singlePaired.pInput1
+ --input2=$singlePaired.pInput2
+ --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=$singlePaired.pParams.pMinInsert
+ --maxInsert=$singlePaired.pParams.pMaxInsert
+ --mateOrient=$singlePaired.pParams.pMateOrient
+ --maxAlignAttempt=$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
+ --strata="None"
+ #end if
+ --offrate=$singlePaired.pParams.pOffrate
+ --seed=$singlePaired.pParams.pSeed
+ #else:
+ --skip="None"
+ --alignLimit="None"
+ --trimH="None"
+ --trimL="None"
+ --mismatchSeed="None"
+ --mismatchQual="None"
+ --seedLen="None"
+ --rounding="None"
+ --maqSoapAlign="None"
+ --tryHard="None"
+ --valAlign="None"
+ --allValAligns="None"
+ --suppressAlign="None"
+ --best="None"
+ --maxBacktracks="None"
+ --strata="None"
+ --offrate="None"
+ --seed="None"
+ --minInsert="None"
+ --maxInsert="None"
+ --mateOrient="None"
+ --maxAlignAttempt="None"
+ --forwardAlign="None"
+ --reverseAlign="None"
+ #end if
+ #end if
</command>
<inputs>
- <conditional name="solidOrSolexa">
- <param name="dataType" type="select" label="Is your data SOLiD or Solexa?">
- <option value="solid">SOLiD</option>
- <option value="solexa">Solexa</option>
+ <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="solid">
- <conditional name="cRefGenomeSource">
- <param name="cGenomeSource" 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="cIndexed">Use a built-in index</option>
- <option value="cHistory">Use one from the history</option>
- </param>
- <when value="cIndexed">
- <param name="cIndex" type="select" label="Select the reference genome" help="if your genome of interest is not listed - contact Galaxy team">
- <options from_file="bowtie_indices_color.loc">
- <column name="value" index="1" />
- <column name="name" index="0" />
- </options>
- </param>
- </when>
- <when value="cHistory">
- <param name="cOwnFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome" />
- <conditional name="cIndexParams">
- <param name="cIndexSettings" type="select" label="Choose whether to use default options for building indices or to set your own">
- <option value="cIndexPreSet">Default</option>
- <option value="cIndexFull">Set your own</option>
- </param>
- <when value="cIndexPreSet" />
- <when value="cIndexFull">
- <conditional name="cAutoBehavior">
- <param name="cAutoB" 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="cAuto">Automatic behavior</option>
- <option value="cSet">Set values (sets --noauto and allows others to be set)</option>
- </param>
- <when value="cAuto" />
- <when value="cSet">
- <param name="cPacked" type="select" label="Whether or not to use a packed representation for DNA strings (-p)">
- <option value="unpacked">Use regular representation</option>
- <option value="packed">Use packed representation</option>
- </param>
- <param name="cBmax" 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="cBmaxdivn" 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="cDcv" type="integer" value="1024" label="The period for the difference-cover sample (--dcv)" />
- </when>
- </conditional>
- <param name="cNodc" 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 (a very repetitive reference)">
- <option value="dc">Use difference-cover sample</option>
- <option value="nodc">Disable difference-cover sample</option>
+ <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_file="bowtie_indices.loc">
+ <column name="value" index="1" />
+ <column name="name" index="0" />
+ </options>
+ </param>
+ </when>
+ <when value="history">
+ <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a 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">
+ <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 (-p)">
+ <option value="unpacked">Use regular representation</option>
+ <option value="packed">Use packed representation</option>
</param>
- <param name="cNoref" 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 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 (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="fastqsanger" 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 arguments 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" />
+ <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>
- <param name="cOffrate" type="integer" value="5" label="How many rows get marked during annotation of some or all of the Burrows-Wheeler rows (-o)" />
- <param name="cFtab" 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="cNtoa" 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>
+ </when>
+ </conditional> <!-- bestOption -->
+ <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 -->
+ <when value="paired">
+ <param name="pInput1" type="data" format="fastqsanger" label="Forward FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
+ <param name="pInput2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
+ <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="pMaxInsert" type="integer" value="250" 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="rf">RF</option>
+ <option value="ff">FF (for SOLiD)</option>
+ </param>
+ <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" />
+ <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>
- <param name="cEndian" 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="cSeed" type="integer" value="-1" label="Seed for the pseudorandom number generator (--seed)" help="Use -1 to use default" />
- <param name="cCutoff" type="integer" value="-1" label="Number of first bases of the reference sequence to index (--cutoff)" help="Use -1 to use default" />
- </when> <!-- cIndexFull -->
- </conditional> <!-- cIndexParams -->
- </when> <!-- cHistory -->
- </conditional> <!-- cRefGenomeSource -->
- <conditional name="cSinglePaired">
- <param name="cSPaired" type="select" label="Is this library mate-paired?">
- <option value="cSingle">Single-end</option>
- <option value="cPaired">Paired-end</option>
- </param>
- <when value="cSingle">
- <param name="csInput1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
- <conditional name="csParams">
- <param name="csSettingsType" 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="csPreSet">Commonly used</option>
- <option value="csFull">Full parameter list</option>
- </param>
- <when value="csPreSet" />
- <when value="csFull">
- <param name="csSkip" type="integer" value="0" label="Skip the first n reads (-s)" />
- <param name="csAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" />
- <param name="csTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
- <param name="csTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
- <param name="csMismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
- <param name="csMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" />
- <param name="csSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" />
- <param name="csRounding" 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="csMaqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" />
- <param name="csTryHard" 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="csValAlign" type="integer" value="1" label="Report up to n valid arguments per read (-k)" />
- <param name="csAllValAligns" 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="csSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m)" help="-1 for no limit" />
- <conditional name="csBestOption">
- <param name="csBest" 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="csNoBest">Do not use best</option>
- <option value="csDoBest">Use best</option>
- </param>
- <when value="csNoBest">
- <param name="csnMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
- </when>
- <when value="csDoBest">
- <param name="csdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
- <param name="csdStrata" 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> <!-- csBestOption -->
- <param name="csOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
- <param name="csSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
- <param name="csSnpphred" 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="csSnpfrac" 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="csKeepends" type="select" label="Keep the extreme-ends nucleotides and qualities rather than trimming them (--keepends)">
- <option value="doKeepends">Keep ends</option>
- <option value="noKeepends">Trim ends</option>
- </param>
- </when> <!-- csFull -->
- </conditional> <!-- csParams -->
- </when> <!-- cSingle -->
- <when value="cPaired">
- <param name="cpInput1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
- <param name="cpInput2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
- <conditional name="cpParams">
- <param name="cpSettingsType" 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="cpPreSet">Commonly used</option>
- <option value="cpFull">Full parameter list</option>
- </param>
- <when value="cpPreSet" />
- <when value="cpFull">
- <param name="cpSkip" type="integer" value="0" label="Skip the first n pairs (-s)" />
- <param name="cpAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" />
- <param name="cpTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
- <param name="cpTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
- <param name="cpMismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
- <param name="cpMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" />
- <param name="cpSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" />
- <param name="cpRounding" 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="cpMaqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" />
- <param name="cpMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" />
- <param name="cpMaxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments (-X)" />
- <param name="cpMateOrient" 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="rf">RF</option>
- <option value="ff">FF</option>
- </param>
- <param name="cpMaxAlignAttempt" 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="cpForwardAlign" 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="cpReverseAlign" 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="cpTryHard" 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="cpValAlign" type="integer" value="1" label="Report up to n valid arguments per pair (-k)" />
- <param name="cpAllValAligns" 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="cpSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a pair if more than n reportable alignments exist (-m)" help="-1 for no limit" />
- <conditional name="cpBestOption">
- <param name="cpBest" 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="cpNoBest">Do not use best</option>
- <option value="cpDoBest">Use best</option>
- </param>
- <when value="cpNoBest">
- <param name="cpnMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
- </when>
- <when value="cpDoBest">
- <param name="cpdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
- <param name="cpdStrata" 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> <!-- cpBestOption -->
- <param name="cpOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
- <param name="cpSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
- <param name="cpSnpphred" 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="cpSnpfrac" 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="cpKeepends" type="select" label="Keep the extreme-ends nucleotides and qualities rather than trimming them (--keepends)">
- <option value="doKeepends">Keep ends</option>
- <option value="noKeepends">Trim ends</option>
- </param>
- </when> <!-- cpFull -->
- </conditional> <!-- cpParams -->
- </when> <!-- cPaired -->
- </conditional> <!-- cSinglePaired -->
- </when> <!-- solid -->
- <when value="solexa">
- <conditional name="xRefGenomeSource">
- <param name="xGenomeSource" 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="xIndexed">Use a built-in index</option>
- <option value="xHistory">Use one from the history</option>
- </param>
- <when value="xIndexed">
- <param name="xIndex" type="select" label="Select the reference genome" help="if your genome of interest is not listed - contact Galaxy team">
- <options from_file="bowtie_indices.loc">
- <column name="value" index="1" />
- <column name="name" index="0" />
- </options>
- </param>
- </when>
- <when value="xHistory">
- <param name="xOwnFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome" />
- <conditional name="xIndexParams">
- <param name="xIndexSettings" type="select" label="Choose whether to use default options for building indices or to set your own">
- <option value="xIndexPreSet">Default</option>
- <option value="xIndexFull">Set your own</option>
- </param>
- <when value="xIndexPreSet" />
- <when value="xIndexFull">
- <conditional name="xAutoBehavior">
- <param name="xAutoB" 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="xAuto">Automatic behavior</option>
- <option value="xSet">Set values (sets --noauto and allows others to be set)</option>
- </param>
- <when value="xAuto" />
- <when value="xSet">
- <param name="xPacked" type="select" label="Whether or not to use a packed representation for DNA strings (-p)">
- <option value="unpacked">Use regular representation</option>
- <option value="packed">Use packed representation</option>
- </param>
- <param name="xBmax" 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="xBmaxdivn" 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="xDcv" type="integer" value="1024" label="The period for the difference-cover sample (--dcv)" />
- </when>
- </conditional>
- <param name="xNodc" 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 (a very repetitive reference)">
- <option value="dc">Use difference-cover sample</option>
- <option value="nodc">Disable difference-cover sample</option>
- </param>
- <param name="xNoref" 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="xOffrate" type="integer" value="5" label="How many rows get marked during annotation of some or all of the Burrows-Wheeler rows (-o)" />
- <param name="xFtab" 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="xNtoa" 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="xEndian" 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="xSeed" type="integer" value="-1" label="Seed for the pseudorandom number generator (--seed)" help="Use -1 to use default" />
- <param name="xCutoff" type="integer" value="-1" label="Number of first bases of the reference sequence to index (--cutoff)" help="Use -1 to use default" />
- </when> <!-- xIndexFull -->
- </conditional> <!-- xIndexParams -->
- </when> <!-- xHistory -->
- </conditional> <!-- xRefGenomeSource -->
- <conditional name="xSinglePaired">
- <param name="xSPaired" type="select" label="Is this library mate-paired?">
- <option value="xSingle">Single-end</option>
- <option value="xPaired">Paired-end</option>
- </param>
- <when value="xSingle">
- <param name="xsInput1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
- <conditional name="xsParams">
- <param name="xsSettingsType" 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="xsPreSet">Commonly used</option>
- <option value="xsFull">Full parameter list</option>
- </param>
- <when value="xsPreSet" />
- <when value="xsFull">
- <param name="xsSkip" type="integer" value="0" label="Skip the first n reads (-s)" />
- <param name="xsAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" />
- <param name="xsTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
- <param name="xsTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
- <param name="xsMismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
- <param name="xsMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" />
- <param name="xsSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" />
- <param name="xsRounding" 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="xsMaqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" />
- <param name="xsTryHard" 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="xsValAlign" type="integer" value="1" label="Report up to n valid arguments per read (-k)" />
- <param name="xsAllValAligns" 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="xsSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m)" help="-1 for no limit" />
- <conditional name="xsBestOption">
- <param name="xsBest" 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="xsNoBest">Do not use best</option>
- <option value="xsDoBest">Use best</option>
- </param>
- <when value="xsNoBest">
- <param name="xsnMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
- </when>
- <when value="xsDoBest">
- <param name="xsdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
- <param name="xsdStrata" 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> <!-- xsBestOption -->
- <param name="xsOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
- <param name="xsSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
- </when> <!-- xsFull -->
- </conditional> <!-- xsParams -->
- </when> <!-- xSingle -->
- <when value="xPaired">
- <param name="xpInput1" type="data" format="fastqsanger" label="Forward FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
- <param name="xpInput2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
- <conditional name="xpParams">
- <param name="xpSettingsType" 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="xpPreSet">Commonly used</option>
- <option value="xpFull">Full parameter list</option>
- </param>
- <when value="xpPreSet" />
- <when value="xpFull">
- <param name="xpSkip" type="integer" value="0" label="Skip the first n pairs (-s)" />
- <param name="xpAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" />
- <param name="xpTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
- <param name="xpTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
- <param name="xpMismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
- <param name="xpMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" />
- <param name="xpSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" />
- <param name="xpRounding" 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="xpMaqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" />
- <param name="xpMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" />
- <param name="xpMaxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments (-X)" />
- <param name="xpMateOrient" 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="rf">RF</option>
- <option value="ff">FF</option>
- </param>
- <param name="xpMaxAlignAttempt" 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="xpForwardAlign" 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="xpReverseAlign" 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="xpTryHard" 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="xpValAlign" type="integer" value="1" label="Report up to n valid arguments per pair (-k)" />
- <param name="xpAllValAligns" 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="xpSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a pair if more than n reportable alignments exist (-m)" help="-1 for no limit" />
- <conditional name="xpBestOption">
- <param name="xpBest" 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="xpNoBest">Do not use best</option>
- <option value="xpDoBest">Use best</option>
- </param>
- <when value="xpNoBest">
- <param name="xpnMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
- </when>
- <when value="xpDoBest">
- <param name="xpdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
- <param name="xpdStrata" 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> <!-- xpBestOption -->
- <param name="xpOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
- <param name="xpSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
- </when> <!-- xpFull -->
- </conditional> <!-- xpParams -->
- </when> <!-- xPaired -->
- </conditional> <!-- xSinglePaired -->
- </when> <!-- solexa -->
- </conditional> <!-- solidOrSolexa -->
+ </when>
+ </conditional>
+ <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="true" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information" />
</inputs>
<outputs>
@@ -784,225 +387,93 @@
<test>
<!--
Bowtie command:
- bowtie -p 4 -S +sam-nohead -q -C chrM_color test-data/bowtie_in1.fastqsanger > test-data/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="dataType" value="solid" />
- <param name="cGenomeSource" value="cIndexed" />
- <param name="cIndex" value="equCab2chrM" />
- <param name="cSPaired" value="cSingle" />
- <param name="csInput1" ftype="fastqsanger" value="bowtie_in1.fastqsanger" />
- <param name="csSettingsType" value="csPreSet" />
- <param name="suppressHeader" value="true" />
- <output name="output" ftype="sam" file="bowtie_out1.sam" />
- </test>
- <test>
- <!--
- Bowtie command:
bowtie -p 4 -S +sam-nohead -q chrM_base test-data/bowtie_in2.fastqsanger > test-data/bowtie_out2.sam
-p is the number of threads, which is hardcoded above. You need to replace the + with 2 dashes.
chrM_base needs to be the base location/name of the index files.
-->
- <param name="dataType" value="solexa" />
- <param name="xGenomeSource" value="xIndexed" />
- <param name="xIndex" value="equCab2chrM" />
- <param name="xSPaired" value="xSingle" />
- <param name="xsInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
- <param name="xsSettingsType" value="xsPreSet" />
+ <param name="genomeSource" value="indexed" />
+ <param name="index" value="equCab2chrM" />
+ <param name="sPaired" value="single" />
+ <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
+ <param name="sSettingsType" value="preSet" />
<param name="suppressHeader" value="true" />
<output name="output" ftype="sam" file="bowtie_out2.sam" />
</test>
<test>
<!--
Bowtie command:
- bowtie-build -f -C test-data/chr_m.fasta chrM_color
- bowtie -n 2 -e 70 -l 28 -X 250 +fr +pairtries 100 +maxbts 125 -k 1 -C +snpfrac 0.001 +col-keepends -p 4 -S +sam-nohead -q chrM_color -1 test-data/bowtie_in3.fastqsanger -2 test-data/bowtie_in4.fastqsanger > test-data/bowtie_out3.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="dataType" value="solid" />
- <param name="cGenomeSource" value="cHistory" />
- <param name="cOwnFile" value="chr_m.fasta" />
- <param name="cIndexSettings" value="cIndexPreSet" />
- <param name="cSPaired" value="cPaired" />
- <param name="cpInput1" ftype="fastqsanger" value="bowtie_in3.fastqsanger" />
- <param name="cpInput2" ftype="fastqsanger" value="bowtie_in4.fastqsanger" />
- <param name="cpSettingsType" value="cpFull" />
- <param name="cpSkip" value="0" />
- <param name="cpAlignLimit" value="-1" />
- <param name="cpTrimH" value="0" />
- <param name="cpTrimL" value="0" />
- <param name="cpMismatchSeed" value="2" />
- <param name="cpMismatchQual" value="70" />
- <param name="cpSeedLen" value="28" />
- <param name="cpRounding" value="round" />
- <param name="cpMaqSoapAlign" value="-1" />
- <param name="cpMinInsert" value="0" />
- <param name="cpMaxInsert" value="250" />
- <param name="cpMateOrient" value="fr" />
- <param name="cpMaxAlignAttempt" value="100" />
- <param name="cpForwardAlign" value="forward" />
- <param name="cpReverseAlign" value="reverse" />
- <param name="cpTryHard" value="noTryHard" />
- <param name="cpValAlign" value="1" />
- <param name="cpAllValAligns" value="noAllValAligns" />
- <param name="cpSuppressAlign" value="-1" />
- <param name="cpBest" value="cpNoBest" />
- <param name="cpnMaxBacktracks" value="125" />
- <param name="cpOffrate" value="-1" />
- <param name="cpSeed" value="-1" />
- <param name="cpSnpphred" value="-1" />
- <param name="cpSnpfrac" value="0.001" />
- <param name="cpKeepends" value="doKeepends" />
- <param name="suppressHeader" value="true" />
- <output name="output" ftype="sam" file="bowtie_out3.sam" />
- </test>
- <test>
- <!--
- Bowtie command:
bowtie-build -f test-data/chr_m.fasta chrM_base
bowtie -n 2 -e 70 -l 28 -X 250 +fr +pairtries 100 +maxbts 800 -k 1 +best -p 4 -S +sam-nohead -q chrM_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > test-data/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="dataType" value="solexa" />
- <param name="xGenomeSource" value="xHistory" />
- <param name="xOwnFile" value="chr_m.fasta" />
- <param name="xIndexSettings" value="xIndexPreSet" />
- <param name="xSPaired" value="xPaired" />
- <param name="xpInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
- <param name="xpInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
- <param name="xpSettingsType" value="xpFull" />
- <param name="xpSkip" value="0" />
- <param name="xpAlignLimit" value="-1" />
- <param name="xpTrimH" value="0" />
- <param name="xpTrimL" value="0" />
- <param name="xpMismatchSeed" value="2" />
- <param name="xpMismatchQual" value="70" />
- <param name="xpSeedLen" value="28" />
- <param name="xpRounding" value="round" />
- <param name="xpMaqSoapAlign" value="-1" />
- <param name="xpMinInsert" value="0" />
- <param name="xpMaxInsert" value="250" />
- <param name="xpMateOrient" value="fr" />
- <param name="xpMaxAlignAttempt" value="100" />
- <param name="xpForwardAlign" value="forward" />
- <param name="xpReverseAlign" value="reverse" />
- <param name="xpTryHard" value="noTryHard" />
- <param name="xpValAlign" value="1" />
- <param name="xpAllValAligns" value="noAllValAligns" />
- <param name="xpSuppressAlign" value="-1" />
- <param name="xpBest" value="xpDoBest" />
- <param name="xpdMaxBacktracks" value="800" />
- <param name="xpdStrata" value="noStrata" />
- <param name="xpOffrate" value="-1" />
- <param name="xpSeed" value="-1" />
+ <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="fastqsanger" value="bowtie_in5.fastqsanger" />
+ <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
+ <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="pMaxInsert" value="250" />
+ <param name="pMateOrient" value="fr" />
+ <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="pBest" value="doBest" />
+ <param name="pdMaxBacktracks" value="800" />
+ <param name="pdStrata" value="noStrata" />
+ <param name="pOffrate" value="-1" />
+ <param name="pSeed" value="-1" />
<param name="suppressHeader" value="true" />
<output name="output" ftype="sam" file="bowtie_out4.sam" />
</test>
-<!-- Comment out tests 5 and 6 because they are failing for an unknown reason
+<!-- Comment out test 3 because they are failing for an unknown reason -->
<test>
---> <!--
- Bowtie command:
- bowtie -n 2 -e 70 -l 28 +maxbts 125 -k 1 -C +snpfrac 0.001 +col-keepends -p 4 -S +sam-nohead -q chrM_color test-data/bowtie_in1.fastqsanger > test-data/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="dataType" value="solid" />
- <param name="cGenomeSource" value="cIndexed" />
- <param name="cIndex" value="equCab2chrM" />
- <param name="cSPaired" value="cSingle" />
- <param name="csInput1" value="bowtie_in1.fastqsanger" />
- <param name="csSettingsType" value="csFull" />
- <param name="csSkip" value="0" />
- <param name="csAlignLimit" value="-1" />
- <param name="csTrimH" value="0" />
- <param name="csTrimL" value="0" />
- <param name="csMismatchSeed" value="2" />
- <param name="csMismatchQual" value="70" />
- <param name="csSeedLen" value="28" />
- <param name="csRounding" value="round" />
- <param name="csMaqSoapAlign" value="-1" />
- <param name="csTryHard" value="noTryHard" />
- <param name="csValAlign" value="1" />
- <param name="csAllValAligns" value="noAllValAligns" />
- <param name="csSuppressAlign" value="-1" />
- <param name="csBest" value="csNoBest" />
- <param name="csnMaxBacktracks" value="125" />
- <param name="csOffrate" value="-1" />
- <param name="csSeed" value="-1" />
- <param name="csSnpphred" value="-1" />
- <param name="csSnpfrac" value="0.001" />
- <param name="csKeepends" value="doKeepends" />
- <param name="suppressHeader" value="true" />
- <output name="output" ftype="sam" file="bowtie_out5.sam" />
- </test>
- <test>
---> <!--
+ <!--
Bowtie command:
bowtie -n 2 -e 70 -l 28 -k 1 +maxbts 125 -y -p 4 -S +sam-nohead -q chrM_base test-data/bowtie_in2.fastqsanger > test-data/bowtie_out6.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="dataType" value="solexa" />
- <param name="xGenomeSource" value="xIndexed" />
- <param name="xIndex" value="equCab2chrM" />
- <param name="xSPaired" value="xSingle" />
- <param name="xsInput1" value="bowtie_in2.fastqsanger" />
- <param name="xsSettingsType" value="xsFull" />
- <param name="xsSkip" value="0" />
- <param name="xsAlignLimit" value="-1" />
- <param name="xsTrimH" value="0" />
- <param name="xsTrimL" value="0" />
- <param name="xsMismatchSeed" value="2" />
- <param name="xsMismatchQual" value="70" />
- <param name="xsSeedLen" value="28" />
- <param name="xsRounding" value="round" />
- <param name="xsMaqSoapAlign" value="-1" />
- <param name="xsTryHard" value="doTryHard" />
- <param name="xsValAlign" value="1" />
- <param name="xsAllValAligns" value="noAllValAligns" />
- <param name="xsSuppressAlign" value="-1" />
- <param name="xsBest" value="xsNoBest" />
- <param name="xsnMaxBacktracks" value="125" />
- <param name="xsOffrate" value="-1" />
- <param name="xsSeed" value="-1" />
+ <param name="genomeSource" value="indexed" />
+ <param name="index" value="equCab2chrM" />
+ <param name="sPaired" value="single" />
+ <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
+ <param name="sSettingsType" value="full" />
+ <param name="sSkip" value="0" />
+ <param name="sAlignLimit" value="-1" />
+ <param name="sTrimH" value="0" />
+ <param name="sTrimL" value="0" />
+ <param name="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="doTryHard" />
+ <param name="sValAlign" value="1" />
+ <param name="sAllValAligns" value="noAllValAligns" />
+ <param name="sSuppressAlign" value="-1" />
+ <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_out6.sam" />
</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 -p 4 -S +sam-nohead -q -C chrM_color -1 test-data/bowtie_in3.fastqsanger -2 test-data/bowtie_in4.fastqsanger > test-data/bowtie_out7.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="dataType" value="solid" />
- <param name="cGenomeSource" value="cHistory" />
- <param name="cOwnFile" value="chr_m.fasta" />
- <param name="cIndexSettings" value="cIndexFull" />
- <param name="cAutoB" value="cSet" />
- <param name="cPacked" value="unpacked" />
- <param name="cBmax" value="-1" />
- <param name="cBmaxdivn" value="4" />
- <param name="cDcv" value="1024" />
- <param name="cNodc" value="dc" />
- <param name="cNoref" value="ref" />
- <param name="cOffrate" value="5" />
- <param name="cFtab" value="10" />
- <param name="cNtoa" value="no" />
- <param name="cEndian" value="little" />
- <param name="cSeed" value="-1" />
- <param name="cCutoff" value="-1" />
- <param name="cSPaired" value="cPaired" />
- <param name="cpInput1" ftype="fastqsanger" value="bowtie_in3.fastqsanger" />
- <param name="cpInput2" ftype="fastqsanger" value="bowtie_in4.fastqsanger" />
- <param name="cpSettingsType" value="cpPreSet" />
- <param name="suppressHeader" value="true" />
- <output name="output" ftype="sam" file="bowtie_out7.sam" />
- </test>
<test>
<!--
Bowtie command:
@@ -1011,23 +482,22 @@
-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="dataType" value="solexa" />
- <param name="xGenomeSource" value="xHistory" />
- <param name="xOwnFile" value="chr_m.fasta" />
- <param name="xIndexSettings" value="xIndexFull" />
- <param name="xAutoB" value="xAuto" />
- <param name="xNodc" value="dc" />
- <param name="xNoref" value="ref" />
- <param name="xOffrate" value="5" />
- <param name="xFtab" value="10" />
- <param name="xNtoa" value="no" />
- <param name="xEndian" value="little" />
- <param name="xSeed" value="-1" />
- <param name="xCutoff" value="-1" />
- <param name="xSPaired" value="xPaired" />
- <param name="xpInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
- <param name="xpInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
- <param name="xpSettingsType" value="xpPreSet" />
+ <param name="genomeSource" value="history" />
+ <param name="ownFile" value="chr_m.fasta" />
+ <param name="indexSettings" value="indexFull" />
+ <param name="autoB" value="auto" />
+ <param name="nodc" value="dc" />
+ <param name="noref" value="ref" />
+ <param name="offrate" value="5" />
+ <param name="ftab" value="10" />
+ <param name="ntoa" value="no" />
+ <param name="endian" value="little" />
+ <param name="seed" value="-1" />
+ <param name="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="pSettingsType" value="preSet" />
<param name="suppressHeader" value="true" />
<output name="output" ftype="sam" file="bowtie_out8.sam" />
</test>
diff -r b78de785df21 -r 35d2a31cfbaf tools/sr_mapping/bowtie_wrapper_code.py
--- a/tools/sr_mapping/bowtie_wrapper_code.py Tue Jan 12 15:48:21 2010 -0500
+++ b/tools/sr_mapping/bowtie_wrapper_code.py Tue Jan 12 16:49:02 2010 -0500
@@ -2,19 +2,12 @@
def exec_before_job(app, inp_data, out_data, param_dict, tool):
try:
- try:
- refFile = param_dict[ 'solidOrSolexa' ][ 'cRefGenomeSource' ][ 'cIndex' ].value
- except:
- refFile = param_dict[ 'solidOrSolexa' ][ 'xRefGenomeSource' ][ 'xIndex' ].value
+ refFile = param_dict[ 'refGenomeSource' ][ 'index' ].value
except:
try:
- try:
- refFile = param_dict[ 'solidOrSolexa' ][ 'cRefGenomeSource' ][ 'cOwnFile' ].dbkey
- except:
- refFile = param_dict[ 'solidOrSolexa' ][ 'xRefGenomeSource' ][ 'xOwnFile' ].dbkey
+ refFile = param_dict[ 'refGenomeSource' ][ 'ownFile' ].dbkey
except:
- out_data[ 'output' ].set_dbkey( '?' )
- return
+ refFile = '?'
dbkey = os.path.split( refFile )[1].split( '.' )[0]
# deal with the one odd case
if dbkey.find( 'chrM' ) >= 0 or dbkey.find( 'chr_m' ) >= 0: