| Next changeset 1:bc685d13b637 (2015-11-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef |
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added:
rg_rnaStar.xml test-data/rnastar_test.log test-data/rnastar_test_mapped_reads.bam test-data/rnastar_test_splicejunctions.bed test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger test-data/tophat_test.fa tool-data/rnastar_index.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
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| diff -r 000000000000 -r b2326241bb09 rg_rnaStar.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rg_rnaStar.xml Mon May 18 13:34:13 2015 -0400 |
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| b'@@ -0,0 +1,321 @@\n+<tool id="rna_star" name="rnastar" 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=".*" source="both" level="warning" description="Some stderr/stdout text"/>\n+ </stdio>\n+\n+ <command>\n+ ##\n+ ## Run STAR.\n+ ##\n+ #if str($refGenomeSource.genomeSource) == \'history\':\n+ mkdir -p tempstargenomedir; STAR --runMode genomeGenerate --genomeDir "tempstargenomedir" --genomeFastaFiles "$refGenomeSource.ownFile" --runThreadN 2\n+ #if str($refGenomeSource.geneModel) != \'None\':\n+ --sjdbOverhang "100" --sjdbGTFfile "$refGenomeSource.geneModel"\n+ #if str($refGenomeSource.geneModel.ext) == \'gff3\':\n+ --sjdbGTFtagExonParentTranscript Parent\n+ #end if\n+ #end if\n+ ;\n+ #end if\n+ STAR\n+ ## Can adjust this as appropriate for the system.\n+ --genomeLoad NoSharedMemory\n+ #if str($refGenomeSource.genomeSource) == \'history\':\n+ --genomeDir "tempstargenomedir"\n+ #else\n+ --genomeDir "$refGenomeSource.index.fields.path"\n+ #end if\n+ --readFilesIn $singlePaired.input1\n+ #if str($singlePaired.sPaired) == "paired"\n+ $singlePaired.input2\n+ #end if\n+ --runThreadN 4\n+ #if str($params.settingsType) == "full":\n+ --chimSegmentMin $params.chim_segment_min\n+ --chimScoreMin $params.chim_score_min\n+ #end if\n+\n+ ## may or may not need to generate SAM tags and handle non-canonicals for Cufflinks tools.\n+ $outSAMstrandField $outFilterIntronMotifs $outSAMattributes\n+\n+ ;\n+ ##\n+ ## BAM conversion.\n+ ##\n+\n+ ## Convert aligned reads.\n+ samtools view -Shb Aligned.out.sam | samtools sort - AlignedSorted 2>/dev/null\n+\n+ ## Convert chimeric reads.\n+ #if str($params.settingsType) == "full" and $params.chim_segment_min > 0:\n+ ; samtools view -Shb Chimeric.out.sam | samtools sort - ChimericSorted 2>/dev/null\n+ #end if\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+ 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+ </sanitizer>\n+ </param>\n+ <!-- FASTQ input(s) and options specifically for paired-end data. -->\n+ <conditional name="singlePaired">\n+ <param name="sPaired" type="select" label="Single ended or mate-pair ended reads in this library?">\n+ <option value="single" selected="true">Single-end</option>\n+ <option value="paired">Paired-end</option>\n+ </param>\n+ <when value="single">\n+ <param format="fastqsanger,fastq,fasta" name="input1" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33"/>\n+ </when>\n+ <when value="paired">\n+ <param format="fastqsanger,fastq,fasta" name="input1" type="data" label="RNA-Seq FASTQ file, forward reads"\n+ help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />\n+ <param format="fastqsanger,fastq,fasta" name="input2" type="data" label="RNA-Seq FASTQ file, reverse reads"\n+ help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />\n+ </when>\n+ </conditional>\n+\n+ <!-- Genome source. -->\n+ <conditional name="refGenomeSource">\n+ <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Bu'..b'pare="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+8.2: SAM alignments\n+\n+The number of loci Nmap a read maps to (multi-mapping) is given by NH:i: field.\n+The mapping quality MAPQ (column 5) is 255 for uniquely mapping reads, and int(-10*log10(1-1/Nmap)) for\n+multi-mapping reads. This scheme is same as the one used by Tophat and is compatible with Cufflinks.\n+\n+For multi-mappers, all alignments except one are marked with 0x100 (secondary alignment) in the FLAG\n+column 2. The un-marked alignment is either the best one (i.e. highest scoring), or is randomly selected from\n+the alignments of equal quality.\n+\n+8.2.1: Standard SAM attributes\n+With default --outSAMattributes Standard option the following SAM attributes will be generated:\n+\n+Column 12: NH: number of loci a read (pair) maps to\n+Column 13: IH: alignment index for all alignments of a read\n+Column 14: aS: alignment score\n+Column 15: nM: number of mismatches (does not include indels)\n+\n+8.2.2: Extra SAM attrbiutes\n+If --outSAMattributes All option is used, the following additional attributes will be output:\n+\n+Column 16: jM:B:c,M1,M2,... Intron motifs for all junctions (i.e. N in CIGAR):\n+0: non-canonical; 1:GT/AG, 2: CT/AC, 3: GC/AG, 4: CT/GC, 5: AT/AC, 6: GT/AT.\n+\n+If splice junctions database is used, and a junction is annotated, 20 is added to its motif value.\n+Column 17: jI:B:I,Start1,End1,Start2,End2,... Start and End of introns for all junctions (1-based)\n+\n+Note, that samtools 0.1.18 or later have to be used with these extra attributes.\n+\n+\n+8.2.3: XS SAM strand attribute for Cufflinks/Cuffdiff\n+\n+If you have un-stranded RNA-seq data, and wish to run Cufflinks/Cuffdiff on STAR alignments, you will\n+need to run STAR with --outSAMstrandField intronMotif option, which will generate the XS\n+strand attribute for all alignments that contain splice junctions. The spliced alignments that have undefined\n+strand (i.e. containing only non-canonical junctions) will be suppressed.\n+\n+If you have stranded RNA-seq data, you do not need to use any specific STAR options. Instead, you need\n+to run Cufflinks with the library option --library-type options. For example, cufflinks with\n+library-type fr-firststrand should be used for the b\n+\n+It is recommended to remove the non-canonical junctions for Cufflinks runs using b\n+\n+\n+--outFilterIntronMotifs RemoveNoncanonical\n+filter out alignments that contain non-canonical junctions\n+\n+OR\n+\n+--outFilterIntronMotifs RemoveNoncanonicalUnannotated\n+filter out alignments that contain non-canonical unannotated junctions\n+when using annotated splice junctions database. The annotated non-\n+canonical junctions will be kept.\n+\n+\n+**Attributions**\n+\n+Note that each component has its own license. Good luck with figuring out your obligations.\n+\n+rna_star - see the web site at rna_star_\n+\n+For details, please see the rna_starMS_\n+"STAR: ultrafast universal RNA-seq aligner"\n+A. Dobin et al, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts635\n+\n+Galaxy_ (that\'s what you are using right now!) for gluing everything together\n+\n+Most of the work for this wrapper XML is Jeremy Goecks\' original STAR_ wrapper\n+\n+Minor tweaks to output names to suit our downstream purposes, toolshed automated dependencies\n+and odds and ends of other code and documentation comprising this tool was\n+written by Ross Lazarus and that part is licensed_ the same way as other rgenetics artefacts\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_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+</citations>\n+</tool>\n+\n' |
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| diff -r 000000000000 -r b2326241bb09 test-data/rnastar_test.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test.log Mon May 18 13:34:13 2015 -0400 |
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| @@ -0,0 +1,31 @@ + Started job on | Feb 18 14:00:29 + Started mapping on | Feb 18 14:00:32 + Finished on | Feb 18 14:00:33 + 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 | 99 + Uniquely mapped reads % | 99.00% + Average mapped length | 74.65 + Number of splices: Total | 52 + Number of splices: Annotated (sjdb) | 0 + Number of splices: GT/AG | 52 + Number of splices: GC/AG | 0 + Number of splices: AT/AC | 0 + Number of splices: Non-canonical | 0 + Mismatch rate per base, % | 2.00% + 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 | 0.00% + % of reads unmapped: other | 0.00% |
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| diff -r 000000000000 -r b2326241bb09 test-data/rnastar_test_mapped_reads.bam |
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| Binary file test-data/rnastar_test_mapped_reads.bam has changed |
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| diff -r 000000000000 -r b2326241bb09 test-data/rnastar_test_splicejunctions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test_splicejunctions.bed Mon May 18 13:34:13 2015 -0400 |
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| @@ -0,0 +1,2 @@ +test_chromosome 251 350 1 1 0 27 0 37 +test_chromosome 401 500 1 1 0 25 0 36 |
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| diff -r 000000000000 -r b2326241bb09 test-data/tophat_in2.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_in2.fastqsanger Mon May 18 13:34:13 2015 -0400 |
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@@\n+@test_mRNA_150_290_0/1\n+TCCTAAAAAGTCCGCCTCGGTCTCAGTCTCAAGTAGAAAAAGTCCCGTTGGCGATCCGTCTACGTCCGAGTAAGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_8_197_1/1\n+TCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGACACTACGGGGATGGCGACTAGGACTACGGACGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_82_255_2/1\n+GAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAATATAGTAAAGTAATAGTGGCGTATCGCAAGCTCGACG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_96_238_3/1\n+GATCCGTCTACGTCCGCGTAAGATAATAAAGTACTAGTAGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_72_258_4/1\n+GTAGAAAAAGTCCCGTTGCCCATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_107_286_5/1\n+AAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_122_299_6/1\n+CAAGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGCTCCGTCTACGTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_58_234_7/1\n+AGTCTACGTCCGAGTCAGATAATAAACTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_57_231_8/1\n+GGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCACCGACTGGACTATTTAGGACGATCGGACTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_8_155_9/1\n+TACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTACAGTCGCTGCATCTGACGCTCGAAGTCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_51_237_a/1\n+ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_89_230_b/1\n+TACGTCCGAGTGAGTTAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_105_276_c/1\n+CCTCGATCCCAGTCTCAAGTAGAAAAAGCCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_111_268_d/1\n+CCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAATAATAGTGGCGTAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_151_286_e/1\n+ACGTATTTGGCGCGCGGCCGTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_118_297_f/1\n+AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_16_194_10/1\n+TCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_28_188_11/1\n+TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGAACGGACTTAGAGCGTCAGATGCAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_36_218_12/1\n+GAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGCCTTAGAGCGTCAGATGCAGCGACTGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_105_266_13/1\n+AGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGGATCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_51_248_14/1\n+ACTACGGGGATGACGACGAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGAACTTTTTAGGACGATC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_89_245_15/1\n+AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mR'..b'IIIIIIIIIIIIIII\n+@test_mRNA_33_223_4e/1\n+ACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_172_294_4f/1\n+ACGGATGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTCCTCGGACGTAGACGGATCGCCAACGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_88_257_50/1\n+TAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_3_187_51/1\n+TACTATTTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_9_179_52/1\n+TCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATGGTCCAGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_85_268_53/1\n+TTAGTGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_75_204_54/1\n+ACGGACGGACTTCGAGCCTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_41_236_55/1\n+AGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_56_183_56/1\n+GGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTGGGACGATCGGACT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_87_250_57/1\n+AGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_82_271_58/1\n+GACTTAGAGCGTCAGTTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_6_182_59/1\n+TATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAGTACGGGGATGACGACTAGGACTACGGAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_53_272_5a/1\n+GATCCCAGTGTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_114_277_5b/1\n+GCCTCGATCCCAGTCTCAAGCAGAAAAAGTCCCGTTGCCGTTCCGTCTACCTCCGAGTAAGATAATAAAGTAATA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_39_219_5c/1\n+CTAGGACGTCCCACTATGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGGCTGGACTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_4_191_5d/1\n+CAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGTGTCCTACTGCCCTACTCAGTCCGATCGTCCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_73_259_5e/1\n+CTACGGACGGACTTAGAGCGTCAGATGCTGCGACTGGACTATTTGGGACGATCGGACTGAGGAGGGCAGTAGGAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_87_279_5f/1\n+CCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_125_293_60/1\n+CCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_111_297_61/1\n+AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCGGATCCGTCTACGTCCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_22_173_62/1\n+AGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_116_295_63/1\n+TCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n' 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| diff -r 000000000000 -r b2326241bb09 test-data/tophat_in3.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_in3.fastqsanger Mon May 18 13:34:13 2015 -0400 |
| b |
| b'@@ -0,0 +1,400 @@\n+@test_mRNA_150_290_0/2\n+TACGTATTTGTCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATCCGCCACTATTACTTTATTATCTTACTCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_8_197_1/2\n+GTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_82_255_2/2\n+GACTTAGAGCGTCAGATGCAGCGACTGGACTTTTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_96_238_3/2\n+GATGCAGCGACTGGACTATTTAGGACGATCGGACGGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGACC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_72_258_4/2\n+ACTACGGACGGACTTAGAGCGTCAGATGCAGCAACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_107_286_5/2\n+TGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_122_299_6/2\n+GATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_58_234_7/2\n+GGATGACGCCTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_57_231_8/2\n+CTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCCTAGGGCCGCGCGCCAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_8_155_9/2\n+TGTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_51_237_a/2\n+ATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_89_230_b/2\n+AGCGTCAGGTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_105_276_c/2\n+ACTGGACTATTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_111_268_d/2\n+CTATTTAAGACGTTCCGCCTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_151_286_e/2\n+AAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGATAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_118_297_f/2\n+GGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_16_194_10/2\n+GACTGGATGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACGGACGGACTTAAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_28_188_11/2\n+GCTCGACGCTCAGCCGTAGGGCCTCGCGCCAAATACGAAGCGTCCTACTGCCTTCCTCAGTCCGATCGTCCTAAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_36_218_12/2\n+AGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_105_266_13/2\n+ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_51_248_14/2\n+TCCCGTTGCCGTTCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_89_245_15/2\n+CGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAGAGAAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mR'..b'IIIIIIIIIIIIIII\n+@test_mRNA_33_223_4e/2\n+GAGTTAGATAATAAAGTAATAGTGGCTTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACCTAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_172_294_4f/2\n+CCCGTCCTAAAACGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGCTGCCGACCCGTCTACGTCCGAGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_88_257_50/2\n+GAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_3_187_51/2\n+CTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_9_179_52/2\n+CTGACTAGACTGGAGGCGCTCGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_85_268_53/2\n+CCAGTCTCAAGTAGAAAAAGTCCCGTTGACGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_75_204_54/2\n+TCGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_41_236_55/2\n+TCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_56_183_56/2\n+ACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_87_250_57/2\n+AGAGCGTCAGATGCAGAGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGACGCTACGTATTTGGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_82_271_58/2\n+ATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATGCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_6_182_59/2\n+CGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_53_272_5a/2\n+TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_114_277_5b/2\n+TTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_39_219_5c/2\n+AAGATAATAAAGTAATAGTGGCGTATCGCAAGCTGGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_4_191_5d/2\n+ACTATCTGACGAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTACCATTACGCGGATGACGACTAGGACTACGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_73_259_5e/2\n+AGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATACAGTAATAGTGGCGTATCGCAAGCTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_87_279_5f/2\n+AGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACCGAGGAGGGCAGTAGGACGCTACGTATTTGGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_125_293_60/2\n+CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCTTCGAGGTTGCGATACGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_111_297_61/2\n+CTATTTAGGACGATCGGACTGGGGAGGGCAGTAGGACGCTACGGATTTGGCGCGCGGCCCTACGGCTGAGCGTCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_22_173_62/2\n+GTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTCCAGTCGCTGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_116_295_63/2\n+TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n' |
| b |
| diff -r 000000000000 -r b2326241bb09 test-data/tophat_test.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_test.fa Mon May 18 13:34:13 2015 -0400 |
| b |
| @@ -0,0 +1,14 @@ +>test_chromosome +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +ACTACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCC +ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC +AGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCT +ACGTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCC +GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG +ACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT +GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG +TTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
| b |
| diff -r 000000000000 -r b2326241bb09 tool-data/rnastar_index.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/rnastar_index.loc.sample Mon May 18 13:34:13 2015 -0400 |
| b |
| @@ -0,0 +1,11 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of rna-star indexed sequences data files. You will +#need to create these data files and then create a bowtie_indices.loc +#file similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bowtie2_indices.loc +#file has this format (longer white space characters are TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_base_path> +# +#hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar + |
| b |
| diff -r 000000000000 -r b2326241bb09 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon May 18 13:34:13 2015 -0400 |
| b |
| @@ -0,0 +1,7 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <table name="rnastar_index" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/rnastar_index.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r b2326241bb09 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon May 18 13:34:13 2015 -0400 |
| b |
| @@ -0,0 +1,13 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="rnastar" version="2.4.0d"> + <repository changeset_revision="54c96a529c59" name="package_rnastar_2_4_0d" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <readme> + Installs the STAR wrapper and dependency packages samtools and star - see https://code.google.com/p/rna-star/ + STAR is a very fast mapper for rna-seq giving junctions if the indexes are constructed with a junction library + </readme> + </package> + <package name="samtools" version="0.1.19"> + <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |