2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/29957b479e5d/ changeset: 29957b479e5d user: jgoecks date: 2012-12-18 19:35:56 summary: Bowtie2 wrapper: move read group parameters out of full parameter settings and into own group. affected #: 1 file diff -r e6030730bb85b532534f7229c79751efadcd1eb7 -r 29957b479e5d1e376a2b47dfdf7bd76dcd980fc6 tools/sr_mapping/bowtie2_wrapper.xml --- a/tools/sr_mapping/bowtie2_wrapper.xml +++ b/tools/sr_mapping/bowtie2_wrapper.xml @@ -46,11 +46,11 @@ #end if ## Read group information. - #if $params.readGroup.specReadGroup == "yes" - --rgid="$params.readGroup.rgid" - --rglb="$params.readGroup.rglb" - --rgpl="$params.readGroup.rgpl" - --rgsm="$params.readGroup.rgsm" + #if $readGroup.specReadGroup == "yes" + --rgid="$readGroup.rgid" + --rglb="$readGroup.rglb" + --rgpl="$readGroup.rgpl" + --rgsm="$readGroup.rgsm" #end if </command><inputs> @@ -114,21 +114,21 @@ </when><when value="No" /></conditional> - <conditional name="readGroup"> - <param name="specReadGroup" type="select" label="Specify the read group for this file?"> - <option value="yes">Yes</option> - <option value="no" selected="True">No</option> - </param> - <when value="yes"> - <param name="rgid" type="text" size="25" label="Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group IDs may be modified when merging SAM files in order to handle collisions." /> - <param name="rglb" type="text" size="25" label="Library name (LB)" help="Required if RG specified" /> - <param name="rgpl" type="text" size="25" label="Platform/technology used to produce the reads (PL)" help="Required if RG specified. Valid values : CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT and PACBIO" /> - <param name="rgsm" type="text" size="25" label="Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced" /> - </when> - <when value="no" /> - </conditional></when><!-- full --></conditional><!-- params --> + <conditional name="readGroup"> + <param name="specReadGroup" type="select" label="Specify the read group for this file?"> + <option value="yes">Yes</option> + <option value="no" selected="True">No</option> + </param> + <when value="yes"> + <param name="rgid" type="text" size="25" label="Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group IDs may be modified when merging SAM files in order to handle collisions." /> + <param name="rglb" type="text" size="25" label="Library name (LB)" help="Required if RG specified" /> + <param name="rgpl" type="text" size="25" label="Platform/technology used to produce the reads (PL)" help="Required if RG specified. Valid values : CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT and PACBIO" /> + <param name="rgsm" type="text" size="25" label="Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced" /> + </when> + <when value="no" /> + </conditional><!-- readGroup --></inputs><outputs> https://bitbucket.org/galaxy/galaxy-central/changeset/715063d652ab/ changeset: 715063d652ab user: jgoecks date: 2012-12-18 20:02:12 summary: Add simple read group options to Tophat2 wrapper. affected #: 2 files diff -r 29957b479e5d1e376a2b47dfdf7bd76dcd980fc6 -r 715063d652abc9dc3197617012763284143e7ab2 tools/ngs_rna/tophat2_wrapper.py --- a/tools/ngs_rna/tophat2_wrapper.py +++ b/tools/ngs_rna/tophat2_wrapper.py @@ -83,6 +83,12 @@ parser.add_option( '', '--single-paired', dest='single_paired', help='' ) parser.add_option( '', '--settings', dest='settings', help='' ) + # Read group options. + parser.add_option( '', '--rgid', dest='rgid', help='Read group identifier' ) + parser.add_option( '', '--rglb', dest='rglb', help='Library name' ) + parser.add_option( '', '--rgpl', dest='rgpl', help='Platform/technology used to produce the reads' ) + parser.add_option( '', '--rgsm', dest='rgsm', help='Sample' ) + (options, args) = parser.parse_args() # Color or base space @@ -137,6 +143,15 @@ opts += ' -r %s' % options.mate_inner_dist if options.report_discordant_pairs: opts += ' --report-discordant-pair-alignments' + # Read group options. + if options.rgid: + if not options.rglb or not options.rgpl or not options.rgsm: + stop_err( 'If you want to specify read groups, you must include the ID, LB, PL, and SM tags.' ) + opts += ' --rg-id %s' % options.rgid + opts += ' --rg-library %s' % options.rglb + opts += ' --rg-platform %s' % options.rgpl + opts += ' --rg-sample %s' % options.rgsm + if options.settings == 'preSet': cmd = cmd % ( opts, index_path, reads ) else: diff -r 29957b479e5d1e376a2b47dfdf7bd76dcd980fc6 -r 715063d652abc9dc3197617012763284143e7ab2 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -113,6 +113,14 @@ #end if #end if + + ## Read group information. + #if $readGroup.specReadGroup == "yes" + --rgid="$readGroup.rgid" + --rglb="$readGroup.rglb" + --rgpl="$readGroup.rgpl" + --rgsm="$readGroup.rgsm" + #end if </command><inputs><conditional name="singlePaired"> @@ -291,6 +299,19 @@ </conditional></when><!-- full --></conditional><!-- params --> + <conditional name="readGroup"> + <param name="specReadGroup" type="select" label="Specify read group?"> + <option value="yes">Yes</option> + <option value="no" selected="True">No</option> + </param> + <when value="yes"> + <param name="rgid" type="text" size="25" label="Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group IDs may be modified when merging SAM files in order to handle collisions." /> + <param name="rglb" type="text" size="25" label="Library name (LB)" help="Required if RG specified" /> + <param name="rgpl" type="text" size="25" label="Platform/technology used to produce the reads (PL)" help="Required if RG specified. Valid values : CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT and PACBIO" /> + <param name="rgsm" type="text" size="25" label="Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced" /> + </when> + <when value="no" /> + </conditional><!-- readGroup --></inputs><outputs> @@ -387,6 +408,7 @@ <param name="genomeSource" value="indexed" /><param name="index" value="tophat_test" /><param name="settingsType" value="preSet" /> + <param name="specReadGroup" value="No" /><output name="junctions" file="tophat_out1j.bed" /><output name="accepted_hits" file="tophat_out1h.bam" compare="sim_size" /></test> @@ -404,6 +426,7 @@ <param name="ownFile" ftype="fasta" value="tophat_in1.fasta" /><param name="mate_inner_distance" value="20" /><param name="settingsType" value="preSet" /> + <param name="specReadGroup" value="No" /><output name="junctions" file="tophat2_out2j.bed" /><output name="accepted_hits" file="tophat_out2h.bam" compare="sim_size" /></test> @@ -452,6 +475,7 @@ <param name="multireads" value="4" /><param name="multipairs" value="5" /><param name="ignore_chromosomes" value="chrM"/> + <param name="specReadGroup" value="No" /><output name="insertions" file="tophat_out3i.bed" /><output name="deletions" file="tophat_out3d.bed" /><output name="junctions" file="tophat2_out3j.bed" /> @@ -500,6 +524,7 @@ <param name="multireads" value="4" /><param name="multipairs" value="5" /><param name="ignore_chromosomes" value="chrM"/> + <param name="specReadGroup" value="No" /><output name="junctions" file="tophat2_out4j.bed" /><output name="accepted_hits" file="tophat_out4h.bam" compare="sim_size" /></test> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.