| Previous changeset 0:b2326241bb09 (2015-05-18) Next changeset 2:ace9f5a2b40f (2016-02-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 97a064489364118d108b0dd2cfb4d9bc53080837 |
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modified:
rg_rnaStar.xml tool-data/rnastar_index.loc.sample |
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added:
test-data/rnastar_test2.log test-data/rnastar_test2_mapped_reads.bam test-data/rnastar_test2_splicejunctions.bed |
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| diff -r b2326241bb09 -r bc685d13b637 rg_rnaStar.xml --- a/rg_rnaStar.xml Mon May 18 13:34:13 2015 -0400 +++ b/rg_rnaStar.xml Thu Nov 19 05:34:06 2015 -0500 |
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| b'@@ -1,14 +1,17 @@\n-<tool id="rna_star" name="rnastar" version="2.4.0d">\n+<tool id="rna_star" name="RNA STAR" version="2.4.0d">\n <description>Gapped-read mapper for RNA-seq data</description>\n <requirements>\n <requirement type="package" version="2.4.0d">rnastar</requirement>\n <requirement type="package" version="0.1.19">samtools</requirement>\n </requirements>\n <stdio>\n+ <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>\n+ <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>\n+ <regex match="\\[sam_read1\\] missing header\\? Abort!" source="both" level="fatal"/>\n <regex match=".*" source="both" level="warning" description="Some stderr/stdout text"/>\n </stdio>\n \n- <command>\n+ <command><![CDATA[\n ##\n ## Run STAR.\n ##\n@@ -34,10 +37,13 @@\n #if str($singlePaired.sPaired) == "paired"\n $singlePaired.input2\n #end if\n- --runThreadN 4\n+ --runThreadN \\${GALAXY_SLOTS:-4}\n #if str($params.settingsType) == "full":\n --chimSegmentMin $params.chim_segment_min\n --chimScoreMin $params.chim_score_min\n+ --seedSearchStartLmax $params.seed_search_start_l_max\n+ --alignSJDBoverhangMin $params.align_sjdb_overhang_min\n+ --outFilterScoreMinOverLread $params.out_filter_score_min_over_l_read\n #end if\n \n ## may or may not need to generate SAM tags and handle non-canonicals for Cufflinks tools.\n@@ -49,16 +55,16 @@\n ##\n \n ## Convert aligned reads.\n- samtools view -Shb Aligned.out.sam | samtools sort - AlignedSorted 2>/dev/null\n+ samtools view -Shb Aligned.out.sam | samtools sort - AlignedSorted 2>/dev/null\n \n ## Convert chimeric reads.\n #if str($params.settingsType) == "full" and $params.chim_segment_min > 0:\n- ; samtools view -Shb Chimeric.out.sam | samtools sort - ChimericSorted 2>/dev/null\n+ ; samtools view -Shb Chimeric.out.sam | samtools sort - ChimericSorted 2>/dev/null\n #end if\n- </command>\n+ ]]></command>\n \n <inputs>\n- <param name="jobName" type="text" size="120" value="rna-star run" label="Job narrative (added to output names)"\n+ <param name="jobName" type="text" value="rna-star run" label="Job narrative (added to output names)"\n help="Only letters, numbers and underscores (_) will be retained in this field">\n <sanitizer invalid_char="">\n <valid initial="string.letters,string.digits"><add value="_" /> </valid>\n@@ -109,7 +115,7 @@\n <option value="--outSAMstrandField intronMotif" selected="true">Add XS for cufflinks</option>\n <option value="">No XS added to sam output</option>\n </param>\n- <param name="outFilterIntronMotifs" type="select" label="Canonical junction preparation for unstranded data">\n+ <param name="outFilterIntronMotifs" type="select" label="Canonical junction preparation for unstranded data (--outFilterIntronMotifs)">\n <option value="">No special handling - all non-canonical junctions passed through</option>\n <option value="--outFilterIntronMotifs RemoveNoncanonical" selected="true">Remove all non-canonical junctions for eg cufflinks</option>\n <option value="--outFilterIntronMotifs RemoveNoncanonicalUnannotated">Remove only unannotated non-canonical junctions for eg cufflinks</option>\n@@ -122,10 +128,12 @@\n </param>\n <when value="preSet" />\n <!-- Full/advanced params. -->\n- <when value="full">\n- <param name="chim_segment_min" type="integer" min="0" value="0" label="Minimum chimeric segment length" />\n- <param name="chim_score_min" type="integer" min="0" value="0" label="Minimum total (summed) score of the chimeric segments" />\n-\n+ <when value="full"> \n+ <param name="chim_segm'..b'stqsanger\' ftype=\'fastqsanger\' />\n- <param name=\'jobName\' value=\'rnastar_test\' />\n- <param name=\'genomeSource\' value=\'history\' />\n- <param name=\'ownFile\' value=\'tophat_test.fa\' />\n- <param name=\'sPaired\' value=\'single\' />\n- <param name=\'outSAMattributes\' value=\'--outSAMattributes All\' />\n- <param name=\'outSAMstrandField\' value=\'--outSAMstrandField intronMotif\' />\n- <param name=\'outFilterIntronMotifs\' value=\'--outFilterIntronMotifs RemoveNoncanonical\' />\n- <output name=\'output_log\' file=\'rnastar_test.log\' compare=\'diff\' lines_diff = \'10\'/>\n- <output name=\'splice_junctions\' file="rnastar_test_splicejunctions.bed" compare="sim_size" delta="200"/>\n- <output name=\'mapped_reads\' file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="200" />\n+ <param name=\'input1\' value=\'tophat_in2.fastqsanger\' ftype=\'fastqsanger\' />\n+ <param name=\'jobName\' value=\'rnastar_test\' />\n+ <param name=\'genomeSource\' value=\'history\' />\n+ <param name=\'ownFile\' value=\'tophat_test.fa\' />\n+ <param name=\'sPaired\' value=\'single\' />\n+ <param name=\'outSAMattributes\' value=\'--outSAMattributes All\' />\n+ <param name=\'outSAMstrandField\' value=\'--outSAMstrandField intronMotif\' />\n+ <param name=\'outFilterIntronMotifs\' value=\'--outFilterIntronMotifs RemoveNoncanonical\' />\n+ \n+ <output name=\'output_log\' file=\'rnastar_test.log\' compare=\'diff\' lines_diff = \'10\'/>\n+ <output name=\'splice_junctions\' file="rnastar_test_splicejunctions.bed"/>\n+ <output name=\'mapped_reads\' file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="200" />\n+ </test>\n+ <test>\n+ <param name=\'input1\' value=\'tophat_in2.fastqsanger\' ftype=\'fastqsanger\' />\n+ <param name=\'jobName\' value=\'rnastar_test\' />\n+ <param name=\'genomeSource\' value=\'history\' />\n+ <param name=\'ownFile\' value=\'tophat_test.fa\' />\n+ <param name=\'sPaired\' value=\'single\' />\n+ <param name=\'outSAMattributes\' value=\'--outSAMattributes All\' />\n+ <param name=\'outSAMstrandField\' value=\'--outSAMstrandField intronMotif\' />\n+ <param name=\'outFilterIntronMotifs\' value=\'--outFilterIntronMotifs RemoveNoncanonical\' />\n+ \n+ <param name="settingsType" value="full" />\n+\n+ <param name="chim_segment_min" value="0" />\n+ <param name="chim_score_min" value="0" />\n+ <param name="seed_search_start_l_max" value="25" />\n+ <param name="align_sjdb_overhang_min" value="3" />\n+ <param name="out_filter_score_min_over_l_read" value="0.9" />\n+\n+ <output name=\'output_log\' file=\'rnastar_test2.log\' compare=\'diff\' lines_diff = \'10\'/>\n+ <output name=\'splice_junctions\' file="rnastar_test2_splicejunctions.bed"/>\n+ <output name=\'mapped_reads\' file="rnastar_test2_mapped_reads.bam" compare="sim_size" delta="200" />\n </test>\n </tests>\n <help>\n-\n **What it does**\n Runs the rna star gapped aligner. Suited to paired or single end rna-seq.\n \n@@ -291,7 +321,9 @@\n \n **Attributions**\n \n-Note that each component has its own license. Good luck with figuring out your obligations.\n+Note that each component has its own license:\n+ - RNA STAR: GPLv3\n+ - samtools: MIT/Expat License\n \n rna_star - see the web site at rna_star_\n \n@@ -309,13 +341,13 @@\n \n .. _STAR: https://bitbucket.org/jgoecks/jeremys-code/raw/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml\n .. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/\n-.. _rna_star: http://code.google.com/p/rna-star/\n+.. _rna_star: https://github.com/alexdobin/STAR\n .. _rna_starMS: http://bioinformatics.oxfordjournals.org/content/29/1/15.full\n .. _Galaxy: http://getgalaxy.org\n \n </help>\n <citations>\n- <citation type="doi">doi: 10.1093/bioinformatics/bts635</citation>\n+ <citation type="doi">10.1093/bioinformatics/bts635</citation>\n </citations>\n </tool>\n \n' |
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| diff -r b2326241bb09 -r bc685d13b637 test-data/rnastar_test2.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test2.log Thu Nov 19 05:34:06 2015 -0500 |
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| @@ -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% |
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| diff -r b2326241bb09 -r bc685d13b637 test-data/rnastar_test2_mapped_reads.bam |
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| Binary file test-data/rnastar_test2_mapped_reads.bam has changed |
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| diff -r b2326241bb09 -r bc685d13b637 test-data/rnastar_test2_splicejunctions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test2_splicejunctions.bed Thu Nov 19 05:34:06 2015 -0500 |
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| @@ -0,0 +1,2 @@ +test_chromosome 251 350 1 1 0 23 0 33 +test_chromosome 401 500 1 1 0 24 0 36 |