1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7a9476924daf/ changeset: r5157:7a9476924daf user: dan date: 2011-03-02 17:40:58 summary: Enhance Bowtie wrapper to accept non-sanger variant FASTQ files. affected #: 10 files (7.5 KB) --- a/tools/sr_mapping/bowtie_color_wrapper.xml Wed Mar 02 11:34:36 2011 -0500 +++ b/tools/sr_mapping/bowtie_color_wrapper.xml Wed Mar 02 11:40:58 2011 -0500 @@ -7,7 +7,7 @@ --threads="4" ## Outputs --output=$output - #if $singlePaired == "single" + #if str( $singlePaired.sPaired ) == "single" #if $output_unmapped_reads_l --output_unmapped_reads=$output_unmapped_reads_l #end if --- a/tools/sr_mapping/bowtie_wrapper.py Wed Mar 02 11:34:36 2011 -0500 +++ b/tools/sr_mapping/bowtie_wrapper.py Wed Mar 02 11:40:58 2011 -0500 @@ -67,6 +67,11 @@ import optparse, os, shutil, subprocess, sys, tempfile +#Allow more than Sanger encoded variants +DEFAULT_ASCII_ENCODING = '--phred33-quals' +GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG = { 'fastqsanger':'--phred33-quals', 'fastqillumina':'--phred64-quals', 'fastqsolexa':'--solexa-quals' } +#FIXME: Integer quality scores are supported only when the '--integer-quals' argument is specified to bowtie; this is not currently able to be set in the tool/wrapper/config + def stop_err( msg ): sys.stderr.write( '%s\n' % msg ) sys.exit() @@ -131,6 +136,7 @@ parser.add_option( '-c', '--icutoff', dest='icutoff', help='Number of first bases of the reference sequence to index' ) parser.add_option( '-x', '--indexSettings', dest='index_settings', help='Whether or not indexing options are to be set' ) parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' ) + parser.add_option( '--galaxy_input_format', dest='galaxy_input_format', default="fastqsanger", help='galaxy input format' ) parser.add_option( '--do_not_build_index', dest='do_not_build_index', action="store_true", default=False, help='Flag to specify that provided file is already indexed, use as is' ) (options, args) = parser.parse_args() stdout = '' @@ -255,9 +261,10 @@ mateOrient = '--%s' % options.mateOrient else: mateOrient = '' + quality_score_encoding = GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG.get( options.galaxy_input_format, DEFAULT_ASCII_ENCODING ) if options.params == 'preSet': - aligning_cmds = '-q %s %s -p %s -S %s %s ' % \ - ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace ) + aligning_cmds = '-q %s %s -p %s -S %s %s %s ' % \ + ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace, quality_score_encoding ) else: try: if options.skip and int( options.skip ) > 0: @@ -386,14 +393,15 @@ else: keepends = '' aligning_cmds = '-q %s %s -p %s -S %s %s %s %s %s %s %s %s %s %s %s %s ' \ - '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s' % \ + '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s ' % \ ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace, skip, alignLimit, trimH, trimL, maqSoapAlign, mismatchSeed, mismatchQual, seedLen, rounding, minInsert, maxAlignAttempt, forwardAlign, reverseAlign, maxBacktracks, tryHard, valAlign, allValAligns, suppressAlign, best, strata, offrate, seed, snpphred, snpfrac, keepends, - output_unmapped_reads, output_suppressed_reads ) + output_unmapped_reads, output_suppressed_reads, + quality_score_encoding ) except ValueError, e: # clean up temp dir if os.path.exists( tmp_index_dir ): --- a/tools/sr_mapping/bowtie_wrapper.xml Wed Mar 02 11:34:36 2011 -0500 +++ b/tools/sr_mapping/bowtie_wrapper.xml Wed Mar 02 11:40:58 2011 -0500 @@ -8,13 +8,14 @@ --threads="4" ## Outputs --output=$output - #if $singlePaired == "single" + #if str( $singlePaired.sPaired ) == "single" #if $output_unmapped_reads_l --output_unmapped_reads=$output_unmapped_reads_l #end if #if $output_suppressed_reads_l --output_suppressed_reads=$output_suppressed_reads_l #end if + --galaxy_input_format="${singlePaired.sInput1.ext}" #else #if $output_unmapped_reads_l and $output_unmapped_reads_r --output_unmapped_reads_l=$output_unmapped_reads_l @@ -24,9 +25,10 @@ --output_suppressed_reads_l=$output_suppressed_reads_l --output_suppressed_reads_r=$output_suppressed_reads_r #end if + --galaxy_input_format="${singlePaired.pInput1.ext}" #end if ## Inputs - --dataType="solexa" + --dataType="solexa" ##this indicates that nucleotide base space is used in the wrapper --suppressHeader=$suppressHeader --genomeSource=$refGenomeSource.genomeSource #if $refGenomeSource.genomeSource == "history": @@ -59,7 +61,8 @@ #end if #else ##use pre-built index - --ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] }" + ##--ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] }" + --ref="${ refGenomeSource.index.fields.path }" #end if --paired=$singlePaired.sPaired #if $singlePaired.sPaired == "single": @@ -191,7 +194,7 @@ <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"/> + <param name="sInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/><conditional name="sParams"><param name="sSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"><option value="preSet">Commonly used</option> @@ -245,8 +248,14 @@ </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"/> + <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/> + <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"> + <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">> + <column name="name" index="0"/> + <column name="value" index="0"/> + <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/> + </options> + </param><param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" /><param name="pMateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)"><option value="fr">FR (for Illumina)</option> @@ -333,7 +342,7 @@ </conditional></actions></data> - <data format="fastqsanger" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)"> + <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)"><filter>(( singlePaired['sPaired'] == "single" and singlePaired['sParams']['sSettingsType'] == "full" and @@ -344,13 +353,41 @@ singlePaired['pParams']['pMaxFile'] is True )) </filter> + <actions> + <conditional name="singlePaired.sPaired"> + <when value="single"> + <action type="format"> + <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> + </action> + </when> + <when value="paired"> + <action type="format"> + <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> + </action> + </when> + </conditional> + </actions></data> - <data format="fastqsanger" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)"> + <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)"><filter>singlePaired['sPaired'] == "paired"</filter><filter>singlePaired['pParams']['pSettingsType'] == "full"</filter><filter>singlePaired['pParams']['pMaxFile'] is True</filter> + <actions> + <conditional name="singlePaired.sPaired"> + <when value="single"> + <action type="format"> + <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> + </action> + </when> + <when value="paired"> + <action type="format"> + <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> + </action> + </when> + </conditional> + </actions></data> - <data format="fastqsanger" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)"> + <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)"><filter> (( singlePaired['sPaired'] == "single" and @@ -362,11 +399,39 @@ singlePaired['pParams']['pUnmappedFile'] is True )) </filter> + <actions> + <conditional name="singlePaired.sPaired"> + <when value="single"> + <action type="format"> + <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> + </action> + </when> + <when value="paired"> + <action type="format"> + <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> + </action> + </when> + </conditional> + </actions></data> - <data format="fastqsanger" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)"> + <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)"><filter>singlePaired['sPaired'] == "paired"</filter><filter>singlePaired['pParams']['pSettingsType'] == "full"</filter><filter>singlePaired['pParams']['pUnmappedFile'] is True</filter> + <actions> + <conditional name="singlePaired.sPaired"> + <when value="single"> + <action type="format"> + <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> + </action> + </when> + <when value="paired"> + <action type="format"> + <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> + </action> + </when> + </conditional> + </actions></data></outputs><tests> @@ -379,6 +444,7 @@ chrM_base needs to be the base location/name of the index files. --><param name="genomeSource" value="indexed" /> + <!-- this is the backwards-compatible "unique value" for this index, not an actual path --><param name="index" value="equCab2chrM" /><param name="sPaired" value="single" /><param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" /> @@ -437,6 +503,86 @@ <output name="output_unmapped_reads_l" ftype="fastqsanger" file="bowtie_out8_1.fastq" sort="True" /><output name="output_unmapped_reads_r" ftype="fastqsanger" file="bowtie_out8_2.fastq" sort="True" /></test> + <!-- start testing of non-sanger variant fastq reads --> + <test> + <param name="genomeSource" value="history" /> + <param name="ownFile" value="phiX.fasta" /> + <param name="indexSettings" value="indexPreSet" /> + <param name="sPaired" value="paired" /> + <param name="pInput1" ftype="fastqillumina" value="bowtie_in5.fastqillumina" /> + <param name="pInput2" ftype="fastqillumina" value="bowtie_in6.fastqillumina" /> + <param name="pMaxInsert" value="1000" /> + <param name="pMateOrient" value="ff" /> + <param name="pSettingsType" value="full" /> + <param name="pSkip" value="0" /> + <param name="pAlignLimit" value="-1" /> + <param name="pTrimH" value="0" /> + <param name="pTrimL" value="0" /> + <param name="pMismatchSeed" value="2" /> + <param name="pMismatchQual" value="70" /> + <param name="pSeedLen" value="28" /> + <param name="pRounding" value="round" /> + <param name="pMaqSoapAlign" value="-1" /> + <param name="pMinInsert" value="0" /> + <param name="pMaxAlignAttempt" value="100" /> + <param name="pForwardAlign" value="forward" /> + <param name="pReverseAlign" value="reverse" /> + <param name="pTryHard" value="noTryHard" /> + <param name="pValAlign" value="1" /> + <param name="pAllValAligns" value="noAllValAligns" /> + <param name="pSuppressAlign" value="-1" /> + <param name="pUnmappedFile" value="true" /> + <param name="pMaxFile" value="false" /> + <param name="pBest" value="doBest" /> + <param name="pdMaxBacktracks" value="800" /> + <param name="pdStrata" value="noStrata" /> + <param name="pOffrate" value="-1" /> + <param name="pSeed" value="-1" /> + <param name="suppressHeader" value="true" /> + <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" /> + <output name="output_unmapped_reads_l" ftype="fastqillumna" file="bowtie_out8_1.fastqillumina.sorted" sort="True" /> + <output name="output_unmapped_reads_r" ftype="fastqillumna" file="bowtie_out8_2.fastqillumina.sorted" sort="True" /> + </test> + <test> + <param name="genomeSource" value="history" /> + <param name="ownFile" value="phiX.fasta" /> + <param name="indexSettings" value="indexPreSet" /> + <param name="sPaired" value="paired" /> + <param name="pInput1" ftype="fastqsolexa" value="bowtie_in5.fastqsolexa" /> + <param name="pInput2" ftype="fastqsolexa" value="bowtie_in6.fastqsolexa" /> + <param name="pMaxInsert" value="1000" /> + <param name="pMateOrient" value="ff" /> + <param name="pSettingsType" value="full" /> + <param name="pSkip" value="0" /> + <param name="pAlignLimit" value="-1" /> + <param name="pTrimH" value="0" /> + <param name="pTrimL" value="0" /> + <param name="pMismatchSeed" value="2" /> + <param name="pMismatchQual" value="70" /> + <param name="pSeedLen" value="28" /> + <param name="pRounding" value="round" /> + <param name="pMaqSoapAlign" value="-1" /> + <param name="pMinInsert" value="0" /> + <param name="pMaxAlignAttempt" value="100" /> + <param name="pForwardAlign" value="forward" /> + <param name="pReverseAlign" value="reverse" /> + <param name="pTryHard" value="noTryHard" /> + <param name="pValAlign" value="1" /> + <param name="pAllValAligns" value="noAllValAligns" /> + <param name="pSuppressAlign" value="-1" /> + <param name="pUnmappedFile" value="true" /> + <param name="pMaxFile" value="false" /> + <param name="pBest" value="doBest" /> + <param name="pdMaxBacktracks" value="800" /> + <param name="pdStrata" value="noStrata" /> + <param name="pOffrate" value="-1" /> + <param name="pSeed" value="-1" /> + <param name="suppressHeader" value="true" /> + <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" /> + <output name="output_unmapped_reads_l" ftype="fastqsolexa" file="bowtie_out8_1.fastqsolexa.sorted" sort="True" /> + <output name="output_unmapped_reads_r" ftype="fastqsolexa" file="bowtie_out8_2.fastqsolexa.sorted" sort="True" /> + </test> + <!-- end testing of non-sanger variant fastq reads --><test><!-- Bowtie command: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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