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Changeset 0:93704f98f56e (2016-09-06)

Next changeset 1:0b44456754e2 (2017-04-20)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2

added:
star_fusion.xml
test-data/test1-test1.blastn.tabular
test-data/test1.fa
test-data/test1.fastqsanger
test-data/test1.gtf
test-data/test1.tabular
tool-data/all_fasta.loc.sample
tool_data_table_conf.xml.sample
tool_dependencies.xml

diff -r 000000000000 -r 93704f98f56e star_fusion.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/star_fusion.xml Tue Sep 06 04:55:21 2016 -0400

[

b'@@ -0,0 +1,249 @@\n+<tool id="star_fusion" name="STAR-Fusion" version="0.5.4-2" profile="16.07">\n+ <description>detect fusion genes in RNA-Seq data</description>\n+ <requirements>\n+ \n+ <requirement type="package" version="0.5.4">star-fusion</requirement>\n+ </requirements>\n+\n+ <stdio>\n+ <regex match="command not found" source="stderr" level="fatal"/>\n+ <regex match="EXITING because of INPUT ERROR" source="stderr" level="fatal"/>\n+ <regex match="FATAL ERROR" source="stderr" level="fatal"/>\n+ \n+ <regex match="Warning:" source="stderr" level="warning"/>\n+ <regex match="CMD:" source="stderr" level="warning"/>\n+ \n+ <regex match="-done creating index file:" source="stderr" level="warning"/>\n+ <regex match="-parsing GTF file:" source="stderr" level="warning"/>\n+ <regex match="-building interval tree" source="stderr" level="warning"/>\n+ <regex match="-parsing fusion evidence:" source="stderr" level="warning"/>\n+ <regex match="-mapping reads to genes" source="stderr" level="warning"/>\n+ <regex match="-outputting fusion candidates to file:" source="stderr" level="warning"/>\n+ \n+ <regex match="Process complete" source="stderr" level="warning"/>\n+ </stdio>\n+\n+ <version_command>STAR-Fusion --version 2>&1 | grep version | grep -o -E "software version.*?"</version_command>\n+\n+ <command><![CDATA[\n+ ## 1. ensure the blastn file is provided as *.gz\n+ if file --mime-type \'${blast_pairs}\' | grep -q /gzip\\$; then\n+ gzip_suffix=\'\' ;\n+ else\n+ ## Older versions of gzip do not support the -k option to keep\n+ ## the original file - this should be an universion solution\n+ \n+ gzip -1 -c -- \'${blast_pairs}\' > \'${blast_pairs}.gz\' &&\n+ gzip_suffix=\'.gz\' ;\n+ fi &&\n+ \n+ ## 2. create reference index - using \\$(pwd) is necessary, probably because the perl script changes work directory\n+ ## - @todo once write a decent STAR and STAR Fusion data manager\n+ prep_genome_lib.pl\n+ --genome_fa \'${fasta_type.ownFile}\'\n+ --gtf \'${geneModel}\'\n+ --blast_pairs "${blast_pairs}\\$gzip_suffix"\n+ --CPU \\${GALAXY_SLOTS:-1}\n+ --output_dir "\\$(pwd)/tmp_star_fusion_genome_dir"\n+ &&\n+ \n+ ## 3. Run STAR-Fusion\n+ STAR-Fusion\n+ #if str($input_params.input_source) == "use_chimeric":\n+ --chimeric_junction \'${input_params.chimeric_junction}\'\n+ #else:\n+ --left_fq \'${input_params.left_fq}\'\n+ #if $input_params.right_fq:\n+ --right_fq \'${input_params.right_fq}\'\n+ #end if\n+ #end if\n+\n+ --genome_lib_dir "\\$(pwd)/tmp_star_fusion_genome_dir"\n+\n+ #if str($params.settingsType) == "full":\n+ --min_junction_reads $params.min_junction_reads\n+ --min_sum_frags $params.min_sum_frags\n+ --max_promiscuity $params.max_promiscuity\n+ --min_novel_junction_support $params.min_novel_junction_support\n+ --min_alt_pct_junction $params.min_alt_pct_junction\n+ --aggregate_novel_junction_dist $params.aggregate_novel_junction_dist\n+ --E $params.E\n+ #end if\n+ ]]></command>\n+\n+ <inputs>\n+ <conditional name="input_params">\n+ <param name="input_source"\n+ type="select"\n+ label="Use output from earlier STAR run or let STAR Fusion control running STAR">\n+ <option value="use_chimeric">Use output from earlier STAR</option>\n+ <option value="use_fastq">Let STAR Fusion control running STAR</option>\n+ </param>\n+ <when value="use_chimeric">\n+ <param name="chimeric_junction"\n+ type="data"\n+ format="inte'..b'="${tool.name} on ${on_string}: fusion_candidates.final" from_work_dir="star-fusion.fusion_candidates.final"/>\n+ </outputs>\n+\n+ <tests>\n+ <test>\n+ <param name="input_source" value="use_chimeric" />\n+ <param name="chimeric_junction" ftype="interval" value="test1.tabular" />\n+ <param name="fasta_type_selector" value="history" />\n+ <param name="ownFile" ftype="fasta" value="test1.fa" />\n+ <param name="geneModel" ftype="gtf" value="test1.gtf" />\n+ <param name="blast_pairs" ftype="tabular" value="test1-test1.blastn.tabular" />\n+ <param name="settingsType" value="default" />\n+ \n+ \n+ <output name="output_final">\n+ <assert_contents>\n+ <has_line line="#fusion_name	JunctionReads	SpanningFrags	Splice_type	LeftGene	LeftBreakpoint	RightGene	RightBreakpoint	JunctionReads	SpanningFrags" />\n+ <has_text text="GENE1--GENE2	24	0	INCL_NON_REF_SPLICE	GENE1^GENE1	chr1:240:+	GENE2^GENE2	chr2:241:+" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input_source" value="use_fastq" />\n+ <param name="left_fq" ftype="fastqsanger" value="test1.fastqsanger"/>\n+ <param name="fasta_type_selector" value="history" />\n+ <param name="ownFile" ftype="fasta" value="test1.fa" />\n+ <param name="geneModel" ftype="gtf" value="test1.gtf" />\n+ <param name="blast_pairs" ftype="tabular" value="test1-test1.blastn.tabular" />\n+ <param name="settingsType" value="default" />\n+ \n+ \n+ <output name="output_final">\n+ <assert_contents>\n+ <has_line line="#fusion_name	JunctionReads	SpanningFrags	Splice_type	LeftGene	LeftBreakpoint	RightGene	RightBreakpoint	JunctionReads	SpanningFrags" />\n+ <has_text text="GENE1--GENE2	24	0	INCL_NON_REF_SPLICE	GENE1^GENE1	chr1:240:+	GENE2^GENE2	chr2:241:+" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help>\n+**What it does**\n+\n+STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set.\n+\n+**Input: files required to run STAR-Fusion**\n+ - A genome reference sequence (FASTA-format)\n+ - A corresponding protein-coding gene annotation set (GTF/GFF Format)\n+ - A last-matching gene pairs file - in Galaxy you can create such files with the *ncbi_blast_plus* tool suite containing *blastn*: https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus\n+ - A STAR chimeric/junction output file - this is optional as STAR Fusion can control running STAR as well.\n+\n+The authors of STAR Fusion have made some of these files avaialble at: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/. The gene annotations in each case are restricted to the protein-coding and lincRNA transcripts.\n+More info: https://github.com/STAR-Fusion/STAR-Fusion/wiki\n+\n+ </help>\n+\n+ <citations>\n+ <citation type="bibtex">\n+ @unpublished{star_fusion,\n+ author = {Brian Haas and Nicolas Stransky and Daniel Nicorici}, \n+ title = {STAR-Fusion},\n+ url = {https://github.com/STAR-Fusion/STAR-Fusion}\n+ }\n+ </citation>\n+ </citations>\n+</tool>\n'

diff -r 000000000000 -r 93704f98f56e test-data/test1-test1.blastn.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1-test1.blastn.tabular Tue Sep 06 04:55:21 2016 -0400

@@ -0,0 +1,2 @@
+chr1 chr1 100.00 480 0 0 1 480 1 480 0.0 866
+chr2 chr2 100.00 480 0 0 1 480 1 480 0.0 866

diff -r 000000000000 -r 93704f98f56e test-data/test1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1.fa Tue Sep 06 04:55:21 2016 -0400

@@ -0,0 +1,18 @@
+>chr1
+GACGGACGTATTCCTCTGGCCTCAACGGTTCCTGCTTTCGCTGGGATCCAAGATTGGCAG
+CTGAAACCGCCTTTCCAAAGTGAGTCCTTCGTCTGTGACTAACTGTGCCAAATCGTCTTG
+CAAACTCCTGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATC
+ATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCG
+GTGCAGCCGATTAGGACCATCTAATGCACTTGTTACAAGACTTCTTTTAAATACTTTCTT
+CCTGCCCAGTAGCGGATGATAATGGTTGTTGCCAGCCGGTGTGGAAGGTAACAGCACCGG
+TGCGAGCCTAATGTGCCGTCTCCACCAACACAAGGCTATCCGGTCGTATAATAGGATTCC
+GCAATGGGGTTAGCAAATGGCAGCCTAAACGATATCGGGGACTTGCGATGTACATGCTTT
+>chr2
+TCAACAATAAGCGCTTTTTGTAGGCAGGGGCACCCCCTATCAGTGGCTGCGCCAAAACAT
+CTTCGGATCCCCTTGTCCAATCAAATTGATCGAATTCTTTCATTTAAGACCCTAATATGA
+CATCATTAGTGATTAAATGCCACTCCCAAAATTCTGCCTAGAAATGTTTAAGTTCGCTCC
+ACTAAAGTTGTTTAAAACGACTACTAAATCCGCGTGATAGGGGATTTCATATTTAATCTT
+TTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCG
+CGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGATTCTATAAGA
+TTGCACATTGCGTCTACTTATAAGATGTCTCAACGGCATGCGCAACTTGTGAAGTGCCTA
+CTATCCTTAAACGCATATCTCGCACAGTAACTCCCCAATATGTGAGCATCTGATGTTGCC

diff -r 000000000000 -r 93704f98f56e test-data/test1.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1.fastqsanger Tue Sep 06 04:55:21 2016 -0400

b'@@ -0,0 +1,332 @@\n+@test_chimeric_mRNA_0\n+CAAACTCCTGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_2\n+AACTCCTGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_4\n+CTCCTGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_6\n+CCTGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_8\n+TGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_10\n+ATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_12\n+CCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_14\n+AGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_16\n+TTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_18\n+TAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_20\n+ACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_22\n+TCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_24\n+ACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_26\n+CAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_28\n+AATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_30\n+TTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_32\n+ATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_34\n+AGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_36\n+CCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_38\n+ATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_40\n+ACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_42\n+AGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@te'..b't_chimeric_mRNA_122\n+ATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_124\n+CGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_126\n+TAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_128\n+AGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_130\n+GAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_132\n+ACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_134\n+AGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_136\n+CCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_138\n+GATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_140\n+TCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_142\n+TTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_144\n+AATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_146\n+TGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_148\n+GATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_150\n+TGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_152\n+GCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_154\n+CGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_156\n+CAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_158\n+GGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGATTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_160\n+TGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGATTCTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_162\n+GTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGATTCTATA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_164\n+ATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGATTCTATAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n'

diff -r 000000000000 -r 93704f98f56e test-data/test1.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1.gtf Tue Sep 06 04:55:21 2016 -0400

@@ -0,0 +1,8 @@
+chr1 test gene 140 363 . + . gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1";
+chr1 test transcript 150 353 . + . gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1";
+chr1 test exon 150 353 . + . gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1";
+chr1 test CDS 153 350 . + . gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1";
+chr2 test gene 140 363 . + . gene_id "GENE2"; gene_name "GENE2"; transcript_id "GENE2_t1";
+chr2 test transcript 150 353 . + . gene_id "GENE2"; gene_name "GENE2"; transcript_id "GENE2_t1";
+chr2 test exon 150 353 . + . gene_id "GENE2"; transcript_id "GENE2_t1"; exon_number "1"; gene_name "GENE2";
+chr2 test CDS 153 350 . + . gene_id "GENE2"; transcript_id "GENE2_t1"; exon_number "1"; gene_name "GENE2";

diff -r 000000000000 -r 93704f98f56e test-data/test1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1.tabular Tue Sep 06 04:55:21 2016 -0400

@@ -0,0 +1,24 @@
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_60 181 60M15S 241 60S15M
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_62 183 58M17S 241 58S17M
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_64 185 56M19S 241 56S19M
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_66 187 54M21S 241 54S21M
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_68 189 52M23S 241 52S23M
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_70 191 50M25S 241 50S25M
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_72 193 48M27S 241 48S27M
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_74 195 46M29S 241 46S29M
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_76 197 44M31S 241 44S31M
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_78 199 42M33S 241 42S33M
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_80 201 40M35S 241 40S35M
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_82 203 38M37S 241 38S37M
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_84 205 36M39S 241 36S39M
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_86 207 34M41S 241 34S41M
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_88 209 32M43S 241 32S43M
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_90 211 30M45S 241 30S45M
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_92 213 28M47S 241 28S47M
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_94 215 26M49S 241 26S49M
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_96 217 24M51S 241 24S51M
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_98 219 22M53S 241 22S53M
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_100 221 20M55S 241 20S55M
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_102 223 18M57S 241 18S57M
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_104 225 16M59S 241 16S59M
+chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_106 227 14M61S 241 14S61M

diff -r 000000000000 -r 93704f98f56e tool-data/all_fasta.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample Tue Sep 06 04:55:21 2016 -0400

@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id> <dbkey> <display_name> <file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
+#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#

diff -r 000000000000 -r 93704f98f56e tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Tue Sep 06 04:55:21 2016 -0400

@@ -0,0 +1,7 @@
+<tables>
+    
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+</tables>

diff -r 000000000000 -r 93704f98f56e tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Sep 06 04:55:21 2016 -0400

@@ -0,0 +1,3 @@
+<?xml version="1.0"?>
+<tool_dependency>
+</tool_dependency>