Mercurial > repos > iuc > rgrnastar
changeset 1:bc685d13b637 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 97a064489364118d108b0dd2cfb4d9bc53080837
| author | iuc |
|---|---|
| date | Thu, 19 Nov 2015 05:34:06 -0500 |
| parents | b2326241bb09 |
| children | ace9f5a2b40f |
| files | rg_rnaStar.xml test-data/rnastar_test2.log test-data/rnastar_test2_mapped_reads.bam test-data/rnastar_test2_splicejunctions.bed tool-data/rnastar_index.loc.sample |
| diffstat | 4 files changed, 92 insertions(+), 27 deletions(-) [+] |
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--- a/rg_rnaStar.xml Mon May 18 13:34:13 2015 -0400 +++ b/rg_rnaStar.xml Thu Nov 19 05:34:06 2015 -0500 @@ -1,14 +1,17 @@ -<tool id="rna_star" name="rnastar" version="2.4.0d"> +<tool id="rna_star" name="RNA STAR" version="2.4.0d"> <description>Gapped-read mapper for RNA-seq data</description> <requirements> <requirement type="package" version="2.4.0d">rnastar</requirement> <requirement type="package" version="0.1.19">samtools</requirement> </requirements> <stdio> + <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/> + <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/> + <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/> <regex match=".*" source="both" level="warning" description="Some stderr/stdout text"/> </stdio> - <command> + <command><![CDATA[ ## ## Run STAR. ## @@ -34,10 +37,13 @@ #if str($singlePaired.sPaired) == "paired" $singlePaired.input2 #end if - --runThreadN 4 + --runThreadN \${GALAXY_SLOTS:-4} #if str($params.settingsType) == "full": --chimSegmentMin $params.chim_segment_min --chimScoreMin $params.chim_score_min + --seedSearchStartLmax $params.seed_search_start_l_max + --alignSJDBoverhangMin $params.align_sjdb_overhang_min + --outFilterScoreMinOverLread $params.out_filter_score_min_over_l_read #end if ## may or may not need to generate SAM tags and handle non-canonicals for Cufflinks tools. @@ -49,16 +55,16 @@ ## ## Convert aligned reads. - samtools view -Shb Aligned.out.sam | samtools sort - AlignedSorted 2>/dev/null + samtools view -Shb Aligned.out.sam | samtools sort - AlignedSorted 2>/dev/null ## Convert chimeric reads. #if str($params.settingsType) == "full" and $params.chim_segment_min > 0: - ; samtools view -Shb Chimeric.out.sam | samtools sort - ChimericSorted 2>/dev/null + ; samtools view -Shb Chimeric.out.sam | samtools sort - ChimericSorted 2>/dev/null #end if - </command> + ]]></command> <inputs> - <param name="jobName" type="text" size="120" value="rna-star run" label="Job narrative (added to output names)" + <param name="jobName" type="text" value="rna-star run" label="Job narrative (added to output names)" help="Only letters, numbers and underscores (_) will be retained in this field"> <sanitizer invalid_char=""> <valid initial="string.letters,string.digits"><add value="_" /> </valid> @@ -109,7 +115,7 @@ <option value="--outSAMstrandField intronMotif" selected="true">Add XS for cufflinks</option> <option value="">No XS added to sam output</option> </param> - <param name="outFilterIntronMotifs" type="select" label="Canonical junction preparation for unstranded data"> + <param name="outFilterIntronMotifs" type="select" label="Canonical junction preparation for unstranded data (--outFilterIntronMotifs)"> <option value="">No special handling - all non-canonical junctions passed through</option> <option value="--outFilterIntronMotifs RemoveNoncanonical" selected="true">Remove all non-canonical junctions for eg cufflinks</option> <option value="--outFilterIntronMotifs RemoveNoncanonicalUnannotated">Remove only unannotated non-canonical junctions for eg cufflinks</option> @@ -122,10 +128,12 @@ </param> <when value="preSet" /> <!-- Full/advanced params. --> - <when value="full"> - <param name="chim_segment_min" type="integer" min="0" value="0" label="Minimum chimeric segment length" /> - <param name="chim_score_min" type="integer" min="0" value="0" label="Minimum total (summed) score of the chimeric segments" /> - + <when value="full"> + <param name="chim_segment_min" type="integer" min="0" value="0" label="Minimum chimeric segment length (--chimSegmentMin)" /> + <param name="chim_score_min" type="integer" min="0" value="0" label="Minimum total (summed) score of the chimeric segments (--chimScoreMin)" /> + <param name="seed_search_start_l_max" type="integer" min="0" value="50" label="Defines the search start point through the read - the read is split into pieces no longer than this value (--seedSearchStartLmax)" /> + <param name="align_sjdb_overhang_min" type="integer" value="1" label="Minimum overhang for annotated junctions (--alignSJDBoverhangMin)" /> + <param name="out_filter_score_min_over_l_read" type="float" value="0.66" label="OutFilterScoreMin normalized to read length; sum of mates’ lengths for paired-end reads (--outFilterScoreMinOverLread)" /> </when> </conditional> </inputs> @@ -216,21 +224,43 @@ </outputs> <tests> <test> - <param name='input1' value='tophat_in2.fastqsanger' ftype='fastqsanger' /> - <param name='jobName' value='rnastar_test' /> - <param name='genomeSource' value='history' /> - <param name='ownFile' value='tophat_test.fa' /> - <param name='sPaired' value='single' /> - <param name='outSAMattributes' value='--outSAMattributes All' /> - <param name='outSAMstrandField' value='--outSAMstrandField intronMotif' /> - <param name='outFilterIntronMotifs' value='--outFilterIntronMotifs RemoveNoncanonical' /> - <output name='output_log' file='rnastar_test.log' compare='diff' lines_diff = '10'/> - <output name='splice_junctions' file="rnastar_test_splicejunctions.bed" compare="sim_size" delta="200"/> - <output name='mapped_reads' file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="200" /> + <param name='input1' value='tophat_in2.fastqsanger' ftype='fastqsanger' /> + <param name='jobName' value='rnastar_test' /> + <param name='genomeSource' value='history' /> + <param name='ownFile' value='tophat_test.fa' /> + <param name='sPaired' value='single' /> + <param name='outSAMattributes' value='--outSAMattributes All' /> + <param name='outSAMstrandField' value='--outSAMstrandField intronMotif' /> + <param name='outFilterIntronMotifs' value='--outFilterIntronMotifs RemoveNoncanonical' /> + + <output name='output_log' file='rnastar_test.log' compare='diff' lines_diff = '10'/> + <output name='splice_junctions' file="rnastar_test_splicejunctions.bed"/> + <output name='mapped_reads' file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="200" /> + </test> + <test> + <param name='input1' value='tophat_in2.fastqsanger' ftype='fastqsanger' /> + <param name='jobName' value='rnastar_test' /> + <param name='genomeSource' value='history' /> + <param name='ownFile' value='tophat_test.fa' /> + <param name='sPaired' value='single' /> + <param name='outSAMattributes' value='--outSAMattributes All' /> + <param name='outSAMstrandField' value='--outSAMstrandField intronMotif' /> + <param name='outFilterIntronMotifs' value='--outFilterIntronMotifs RemoveNoncanonical' /> + + <param name="settingsType" value="full" /> + + <param name="chim_segment_min" value="0" /> + <param name="chim_score_min" value="0" /> + <param name="seed_search_start_l_max" value="25" /> + <param name="align_sjdb_overhang_min" value="3" /> + <param name="out_filter_score_min_over_l_read" value="0.9" /> + + <output name='output_log' file='rnastar_test2.log' compare='diff' lines_diff = '10'/> + <output name='splice_junctions' file="rnastar_test2_splicejunctions.bed"/> + <output name='mapped_reads' file="rnastar_test2_mapped_reads.bam" compare="sim_size" delta="200" /> </test> </tests> <help> - **What it does** Runs the rna star gapped aligner. Suited to paired or single end rna-seq. @@ -291,7 +321,9 @@ **Attributions** -Note that each component has its own license. Good luck with figuring out your obligations. +Note that each component has its own license: + - RNA STAR: GPLv3 + - samtools: MIT/Expat License rna_star - see the web site at rna_star_ @@ -309,13 +341,13 @@ .. _STAR: https://bitbucket.org/jgoecks/jeremys-code/raw/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml .. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/ -.. _rna_star: http://code.google.com/p/rna-star/ +.. _rna_star: https://github.com/alexdobin/STAR .. _rna_starMS: http://bioinformatics.oxfordjournals.org/content/29/1/15.full .. _Galaxy: http://getgalaxy.org </help> <citations> - <citation type="doi">doi: 10.1093/bioinformatics/bts635</citation> + <citation type="doi">10.1093/bioinformatics/bts635</citation> </citations> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test2.log Thu Nov 19 05:34:06 2015 -0500 @@ -0,0 +1,31 @@ + Started job on | Jul 23 12:00:42 + Started mapping on | Jul 23 12:00:42 + Finished on | Jul 23 12:00:43 + Mapping speed, Million of reads per hour | 0.36 + + Number of input reads | 100 + Average input read length | 75 + UNIQUE READS: + Uniquely mapped reads number | 89 + Uniquely mapped reads % | 89.00% + Average mapped length | 74.80 + Number of splices: Total | 47 + Number of splices: Annotated (sjdb) | 0 + Number of splices: GT/AG | 47 + Number of splices: GC/AG | 0 + Number of splices: AT/AC | 0 + Number of splices: Non-canonical | 0 + Mismatch rate per base, % | 1.73% + Deletion rate per base | 0.00% + Deletion average length | 0.00 + Insertion rate per base | 0.00% + Insertion average length | 0.00 + MULTI-MAPPING READS: + Number of reads mapped to multiple loci | 1 + % of reads mapped to multiple loci | 1.00% + Number of reads mapped to too many loci | 0 + % of reads mapped to too many loci | 0.00% + UNMAPPED READS: + % of reads unmapped: too many mismatches | 0.00% + % of reads unmapped: too short | 10.00% + % of reads unmapped: other | 0.00%