commit/galaxy-central: 3 new changesets
3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/08320798463e/ Changeset: 08320798463e User: nsoranzo Date: 2013-12-06 11:17:25 Summary: Specify mosaik v. 1.1.0021 (last compatible with the wrapper). Add requirement for samtools. Affected #: 1 file diff -r a29d54619813d5da992b897557162a360b8d610c -r 08320798463e173f61f0b53fbd2db43419d373e2 tools/sr_mapping/mosaik.xml --- a/tools/sr_mapping/mosaik.xml +++ b/tools/sr_mapping/mosaik.xml @@ -1,7 +1,10 @@ <?xml version="1.0"?><tool id="mosaik_wrapper" name="Map with Mosaik" version="1.1.1"><description/> - <requirements><requirement type="package">mosaik</requirement></requirements> + <requirements> + <requirement type="package" version="1.1.0021">mosaik</requirement> + <requirement type="package" version="0.1.18">samtools</requirement> + </requirements><command> #set $processors = '-p ${GALAXY_SLOTS:-4}' #set $lm = '' https://bitbucket.org/galaxy/galaxy-central/commits/5fbc02eff708/ Changeset: 5fbc02eff708 User: nsoranzo Date: 2013-12-06 11:20:56 Summary: Fix for failure preparing job: "NotFound: cannot find 'mfl'" with paired-end library. Add mate FASTQ file to inputs. 'ls' param was not used. Add missing '-mfl ' to MosaikBuild command. Remove always empty $lm variable. Add <version_command>. Affected #: 1 file diff -r 08320798463e173f61f0b53fbd2db43419d373e2 -r 5fbc02eff708cc86afd60a4fa7588c9f72e877b5 tools/sr_mapping/mosaik.xml --- a/tools/sr_mapping/mosaik.xml +++ b/tools/sr_mapping/mosaik.xml @@ -1,28 +1,30 @@ <?xml version="1.0"?> -<tool id="mosaik_wrapper" name="Map with Mosaik" version="1.1.1"> +<tool id="mosaik_wrapper" name="Map with Mosaik" version="1.1.2"><description/><requirements><requirement type="package" version="1.1.0021">mosaik</requirement><requirement type="package" version="0.1.18">samtools</requirement></requirements> + <version_command>MosaikAligner | sed -e 's/\x1b\[[[:digit:]]\{1,2\}\(;[[:digit:]]\{1,2\}\)\{0,1\}m//g' | grep -o 'MosaikAligner [[:digit:].]\{1,\}'</version_command><command> #set $processors = '-p ${GALAXY_SLOTS:-4}' - #set $lm = '' - #if $paired.kind == 'single': - #set $mfl = '' - #set $ls = '' - #else: - #set $ls = '-ls $mfl' - #end if MosaikBuild -fr #if $genomeSource.refGenomeSource == 'indexed': ${genomeSource.indexReference.fields.path} #else: - $genomeSource.historyReference + ${genomeSource.historyReference} #end if - -oa mosaik_ref_file; - MosaikBuild -q $reads $mfl -st $st -out mosaik_reads_file; - MosaikAligner -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file $ls -mm $mm -mhp $mhp -act $act -bw $bw $processors $lm -hs 15; + -oa mosaik_ref_file; + MosaikBuild -q $reads + #if $paired.kind == 'single' + #set $ls_string = '' + #else + -q2 ${paired.reads2} + -mfl ${paired.mfl} + #set $ls_string = '-ls %s' % $paired.ls + #end if + -st $st -out mosaik_reads_file; + MosaikAligner -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file $ls_string -mm $mm -mhp $mhp -act $act -bw $bw $processors -hs 15; MosaikText -in mosaik_aligned_file -$outFormat sam_bam_file; #if str($outFormat) == 'bam': samtools sort sam_bam_file sorted_bam; @@ -50,12 +52,12 @@ <param format="fasta" name="historyReference" type="data" metadata_name="dbkey" label="Select a reference from history"/></when></conditional> - <param format="fastq" name="reads" type="data" label="Fastq Reads File"/> - <param name="outFormat" type="select" label="Output Format"> - <option value="sam">Sam</option> - <option value="bam">Bam</option> + <param format="fastq" name="reads" type="data" label="FASTQ reads file" /> + <param name="outFormat" type="select" label="Output format"> + <option value="sam">SAM</option> + <option value="bam">BAM</option></param> - <param name="st" type="select" label="Sequencing Technology Used"> + <param name="st" type="select" label="Sequencing technology used"><option value="454">454</option><option value="illumina">Illumina</option><option value="solid">Solid</option> @@ -69,14 +71,15 @@ </param><when value="single"/><when value="paired"> - <param name="mfl" type="integer" value="200" label="Insert Size" help="the length between the paired reads"/> - <param name="ls" type="integer" value="50" label="Realignment Window" help="Window size to realign mate pairs that are out of position. Large values slow down performance"/> + <param format="fastq" name="reads2" type="data" label="FASTQ 2nd mate" /> + <param name="mfl" type="integer" value="200" label="Median fragment length" /> + <param name="ls" type="integer" min="0" value="50" label="Local alignment search radius to rescue mates" help="A large value slows down performances" /></when></conditional> - <param name="mm" size="5" type="integer" value="6" label="Mismatches allowed" help="mismatches allowed per sequence"/> - <param name="act" size="5" type="integer" value="35" label="Alignment Candidate Threshold" help="determines which hash regions will be aligned with Smith Waterman"/> - <param name="bw" size="5" type="integer" value="19" label="Smith-Waterman band width"/> - <param name="mhp" size="5" type="integer" value="100" label="Maximum # Of Positions Stored Per Seed" help="number of places in the reference the aligner will try to place a particular hash"/> + <param name="mm" type="integer" value="6" label="Number of mismatches allowed per sequence" /> + <param name="act" type="integer" value="35" label="Alignment candidate threshold" help="Determines which hash regions will be aligned with Smith-Waterman" /> + <param name="bw" type="integer" value="9" label="Smith-Waterman band width" /> + <param name="mhp" type="integer" value="100" label="Maximum number of positions stored per seed" help="Number of places in the reference the aligner will try to place a particular hash" /></inputs><outputs><data format="sam" name="output"> https://bitbucket.org/galaxy/galaxy-central/commits/97c69fcfeaac/ Changeset: 97c69fcfeaac User: dannon Date: 2013-12-17 15:00:44 Summary: Merged in nsoranzo/galaxy-central (pull request #271) Fixes for MOSAIK tool Affected #: 1 file diff -r 3eb13c85bf4140448865328b9c6feaed96d8682f -r 97c69fcfeaac1756a7ad5d92c8ade74b2d611561 tools/sr_mapping/mosaik.xml --- a/tools/sr_mapping/mosaik.xml +++ b/tools/sr_mapping/mosaik.xml @@ -1,25 +1,30 @@ <?xml version="1.0"?> -<tool id="mosaik_wrapper" name="Map with Mosaik" version="1.1.1"> +<tool id="mosaik_wrapper" name="Map with Mosaik" version="1.1.2"><description/> - <requirements><requirement type="package">mosaik</requirement></requirements> + <requirements> + <requirement type="package" version="1.1.0021">mosaik</requirement> + <requirement type="package" version="0.1.18">samtools</requirement> + </requirements> + <version_command>MosaikAligner | sed -e 's/\x1b\[[[:digit:]]\{1,2\}\(;[[:digit:]]\{1,2\}\)\{0,1\}m//g' | grep -o 'MosaikAligner [[:digit:].]\{1,\}'</version_command><command> #set $processors = '-p ${GALAXY_SLOTS:-4}' - #set $lm = '' - #if $paired.kind == 'single': - #set $mfl = '' - #set $ls = '' - #else: - #set $ls = '-ls $mfl' - #end if MosaikBuild -fr #if $genomeSource.refGenomeSource == 'indexed': ${genomeSource.indexReference.fields.path} #else: - $genomeSource.historyReference + ${genomeSource.historyReference} #end if - -oa mosaik_ref_file; - MosaikBuild -q $reads $mfl -st $st -out mosaik_reads_file; - MosaikAligner -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file $ls -mm $mm -mhp $mhp -act $act -bw $bw $processors $lm -hs 15; + -oa mosaik_ref_file; + MosaikBuild -q $reads + #if $paired.kind == 'single' + #set $ls_string = '' + #else + -q2 ${paired.reads2} + -mfl ${paired.mfl} + #set $ls_string = '-ls %s' % $paired.ls + #end if + -st $st -out mosaik_reads_file; + MosaikAligner -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file $ls_string -mm $mm -mhp $mhp -act $act -bw $bw $processors -hs 15; MosaikText -in mosaik_aligned_file -$outFormat sam_bam_file; #if str($outFormat) == 'bam': samtools sort sam_bam_file sorted_bam; @@ -47,12 +52,12 @@ <param format="fasta" name="historyReference" type="data" metadata_name="dbkey" label="Select a reference from history"/></when></conditional> - <param format="fastq" name="reads" type="data" label="Fastq Reads File"/> - <param name="outFormat" type="select" label="Output Format"> - <option value="sam">Sam</option> - <option value="bam">Bam</option> + <param format="fastq" name="reads" type="data" label="FASTQ reads file" /> + <param name="outFormat" type="select" label="Output format"> + <option value="sam">SAM</option> + <option value="bam">BAM</option></param> - <param name="st" type="select" label="Sequencing Technology Used"> + <param name="st" type="select" label="Sequencing technology used"><option value="454">454</option><option value="illumina">Illumina</option><option value="solid">Solid</option> @@ -66,14 +71,15 @@ </param><when value="single"/><when value="paired"> - <param name="mfl" type="integer" value="200" label="Insert Size" help="the length between the paired reads"/> - <param name="ls" type="integer" value="50" label="Realignment Window" help="Window size to realign mate pairs that are out of position. Large values slow down performance"/> + <param format="fastq" name="reads2" type="data" label="FASTQ 2nd mate" /> + <param name="mfl" type="integer" value="200" label="Median fragment length" /> + <param name="ls" type="integer" min="0" value="50" label="Local alignment search radius to rescue mates" help="A large value slows down performances" /></when></conditional> - <param name="mm" size="5" type="integer" value="6" label="Mismatches allowed" help="mismatches allowed per sequence"/> - <param name="act" size="5" type="integer" value="35" label="Alignment Candidate Threshold" help="determines which hash regions will be aligned with Smith Waterman"/> - <param name="bw" size="5" type="integer" value="19" label="Smith-Waterman band width"/> - <param name="mhp" size="5" type="integer" value="100" label="Maximum # Of Positions Stored Per Seed" help="number of places in the reference the aligner will try to place a particular hash"/> + <param name="mm" type="integer" value="6" label="Number of mismatches allowed per sequence" /> + <param name="act" type="integer" value="35" label="Alignment candidate threshold" help="Determines which hash regions will be aligned with Smith-Waterman" /> + <param name="bw" type="integer" value="9" label="Smith-Waterman band width" /> + <param name="mhp" type="integer" value="100" label="Maximum number of positions stored per seed" help="Number of places in the reference the aligner will try to place a particular hash" /></inputs><outputs><data format="sam" name="output"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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