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Commit message:
Upload ctat tools. |
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added:
ctat_gmap_fusion.xml test-data/GMAP/fusion.reads_1_2.final test-data/GMAP/reads_1.fq.gz test-data/GMAP/reads_2.fq.gz test-data/GMAP/transcripts.fa tool-data/ctat_genome_resource_libs.loc.sample tool_data_table_conf.xml.sample |
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| diff -r 000000000000 -r 966ea55e1aae ctat_gmap_fusion.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_gmap_fusion.xml Tue Jul 17 11:52:28 2018 -0400 |
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| @@ -0,0 +1,55 @@ +<tool id="ctat_gmap_fusion" name="ctat_gmap_fusion" version="1.0.0" profile="17.05"> + <description>Fusion-finding Using De novo RNA-Seq Transcript Assemblies</description> + <requirements> + <requirement type="package" version="0.4.0">gmap-fusion</requirement> + </requirements> + <command detect_errors="default"> + GMAP-fusion + -T $assembled_trans + --left_fq $left_input + --right_fq $right_input + --genome_lib_dir "${genome_resource_lib.fields.path}" + --output "subdir" + </command> + <stdio> + <exit_code range="1:" level="fatal" description="Error returned from pipeline" /> + </stdio> + <regex match="Must investigate error above." + source="stderr" + level="fatal" + description="Unknown error encountered" /> + <inputs> + <param format="fasta" name="assembled_trans" type="data" label="Assembled Transcripts (ie. Trinity or DISCASM output)" help="Trinity or DISCASM generated transcript fasta"/> + <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help="Forward strand reads"/> + <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help="Reverse strand reads"/> + <param name="genome_resource_lib" type="select" label="Select a reference genome"> + <options from_data_table="ctat_genome_resource_libs"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No indexes are available" /> + </options> + </param> + </inputs> + <outputs> + <data format="tabular" name="gmapfusion_candidates" label="${tool.name} on ${on_string}: GMAP-fusion candidates" from_work_dir="subdir/GMAP-fusion.final"/> + </outputs> + + <tests> + <test> + <param name="left_input" value="GMAP/reads_1.fq.gz" /> + <param name="right_input" value="GMAP/reads_2.fq.gz" /> + <param name="assembled_trans" value="GMAP/transcripts.fa" /> + <!-- FIX - now that we added the CTAT ref lib path as a parameter, how do we find it for testing? + <param name="genome_resource_lib.fields.path" value="?????" /> + --> + <output name="gmapfusion_candidates" file="GMAP/fusion.reads_1_2.final" /> + </test> + </tests> + + <help> +.. class:: infomark + +GMAP-fusion is a utility for identifying candidate fusion transcripts based on transcript sequences reconstructed via RNA-Seq de novo transcriptome assembly. Please read more here_. + +.. _here: https://github.com/GMAP-fusion/GMAP-fusion/wiki + </help> +</tool> |
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| diff -r 000000000000 -r 966ea55e1aae test-data/GMAP/fusion.reads_1_2.final --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GMAP/fusion.reads_1_2.final Tue Jul 17 11:52:28 2018 -0400 |
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| @@ -0,0 +1,7 @@ +#fusion_name J S trans_acc trans_brkpt geneA chrA coordA geneB chrB coordB junction_type +RPS6KB1--SNF8 10 22 Locus_20_Transcript_1/1_Confidence_1.000_Length_350 156-157 RPS6KB1 chr17 57970686 SNF8 chr17 47021337 ONLY_REF_SPLICE +ACACA--STAC2 9 22 Locus_6_Transcript_1/1_Confidence_1.000_Length_398 170-171 ACACA chr17 35479453 STAC2 chr17 37374426 ONLY_REF_SPLICE +VAPB--IKZF3 1 21 Locus_24_Transcript_1/1_Confidence_1.000_Length_308 168-169 VAPB chr20 56964573 IKZF3 chr17 37934020 ONLY_REF_SPLICE +AHCTF1--NAAA 3 8 Locus_44_Transcript_1/1_Confidence_1.000_Length_339 133-134 AHCTF1 chr1 247094880 NAAA chr4 76846964 ONLY_REF_SPLICE +MED1--ACSF2 4 2 Locus_51_Transcript_1/1_Confidence_1.000_Length_187 88-87 MED1 chr17 37595418 ACSF2 chr17 48548389 ONLY_REF_SPLICE +TOB1--SYNRG 1 1 Locus_26_Transcript_1/1_Confidence_1.000_Length_201 90-91 TOB1 chr17 48943419 SYNRG chr17 35880751 ONLY_REF_SPLICE |
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| diff -r 000000000000 -r 966ea55e1aae test-data/GMAP/reads_1.fq.gz |
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| Binary file test-data/GMAP/reads_1.fq.gz has changed |
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| diff -r 000000000000 -r 966ea55e1aae test-data/GMAP/reads_2.fq.gz |
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| Binary file test-data/GMAP/reads_2.fq.gz has changed |
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| diff -r 000000000000 -r 966ea55e1aae test-data/GMAP/transcripts.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GMAP/transcripts.fa Tue Jul 17 11:52:28 2018 -0400 |
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| b'@@ -0,0 +1,250 @@\n+>Locus_1_Transcript_1/1_Confidence_1.000_Length_106\n+GCCATCTTTTACTGCTGTTGGAACACCAGCTACTGTGACTACCCCTGCCAGCAAGCCCAC\n+TGGCCTGAGCACATGAAGTCCTGCACCCAGTCAGGAGAAGGAGCGC\n+>Locus_2_Transcript_1/1_Confidence_1.000_Length_1407\n+CCCCAACTAAATACTACCGTATGGCCCACCATAATTACCCCCATACTCCTTACACTATTC\n+CTCATCACCCAACTAAAAATATTAAACACAAACTACCACCTACCTCCCTCACCAAAGCCC\n+ATAAAAATAAAAAATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCTGTTCGCTT\n+CATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCTATTTCCCC\n+CTCTATTGATCCCCACCTCCAAATATCTCATCAACAACCGACTAATCACCACCCAACAAT\n+GACTAATCAAACTAACCTCAAAACAAATGATAACCATACACAACACTAAAGGACGAACCT\n+GATCTCTTATACTAGTATCCTTAATCATTTTTATTGCCACAACTAACCTCCTCGGACTCC\n+TGCCTCACTCATTTACACCAACCACCCAACTATCTATAAACCTAGCCATGGCCATCCCCT\n+TATGAGCGGGCGCAGTGATTATAGGCTTTCGCTCTAAGATTAAAAATGCCCTAGCCCACT\n+TCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAGTTATTATCGAAACCATCA\n+GCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTAACCGCTAACATTACTGCAGGCC\n+ACCTACTCATGCACCTAATTGGAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCT\n+CTACACTTATCATCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCT\n+TAATCCAAGCCTACGTTTTCACACTTCTAGTAAGCCTCTACCTGCACGACAACACATAAT\n+GACCCACCAATCACATGCCTATCATATAGTAAAACCCAGCCCATGACCCCTAACAGGGGC\n+CCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATTTCACTTCCACTCCATAAC\n+GCTCCTCATACTAGGCCTACTAACCAACACACTAACCATATACCAATGATGGCGCGATGT\n+AACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATA\n+CGGGATAATCCTATTTATTACCTCAGAAATTTTTTTCTTCGCAGGGTTTTTCTGAGCCTT\n+TTACCACTCCAGCCTAGCCCCTACCCCCCAATTAGGAGGGCACTGGCCCCCAACAGGCAT\n+CACCCCGCTAAATCCCCTAGAAGTCCCACTCCTAAACACATCCGTATTACTCGCATCAGG\n+AGTATCAATCACCTGAGCTCACCATAGTCTAATAGAAAACAACCGAAACCAAATAATTCA\n+AGCACTGCTTATTACAATTTTACTGGGTCTCTATTTTACCCTCCTACAAGCCTCAGAGTA\n+CTTCGAGTCTCCCTTCACCATTTCCGA\n+>Locus_3_Transcript_1/1_Confidence_1.000_Length_351\n+TCGCGGGGACACCGGGGGGGCGCCGGGGGCCTCCCACTTATTCTACACCTCTCATGTCTC\n+TTCACCGTGCCAGACTAGAGTCAAGCTCAACAGGGTCTTCTTTCCCCGCTGATTCCGCCA\n+AGCCCGTTCCCTTGGCTGTGGTTTCGCTGGATAGTAGGTAGGGACAGTGGGAATCTCGTT\n+CATCCATTCATGCGCGTCACTAATTAGATGACGAGGCATTTGGCTACCTTAAGAGAGTCA\n+TAGTTACTCCCGCCGTTTACCCGCGCTTCATTGAATTTCTTCACTTTGACATTCAGAGCA\n+CTGGGCAGAAATCACATCGCGTCAACACCCGCCGGAGGAGGAGACCCCATT\n+>Locus_5_Transcript_1/1_Confidence_1.000_Length_226\n+TCCGCAAGCCTGTGACGGTCCATTCCCGGGCTCGATGCCGGAAAAACACCTTGGCCCGCC\n+GGAAGGGCAGGCACATGGGCATAGGTAAGCGGAAGGGTACAGCCAATGCCCGAATGCCAG\n+AGAAGGTCACATGGATGAGGAGAATGAGGATTTTGCGCCGGCTGCTCAGAAGATACCGTG\n+AATCTAAGAAGATCGATCGCCACATGTATCACAGCCTGTACCTGAA\n+>Locus_6_Transcript_1/1_Confidence_1.000_Length_398\n+GCTTTTTTGACTATGGATCTTTCTCAGAGATTATGCAGCCCTGGGCACAGACTGTGGTGG\n+TTGGTAGAGCCAGGCTAGGAGGAATACCTGTGGGAGTTGTTGCTGTAGAAACCCGAACAG\n+TAGAACTAAGTATCCCAGCTGATCCAGCAAACCTGGATTCTGAAGCCAAGCTCCAGCGAT\n+TCAAGCGCTCCCTCTCCCTCAAGACCATCCTCCGAAGTAAGAGCTTGGAGAACTTCTTCC\n+TTCGCTCGGGCTCTGAGCTCAAGTGCCCCACCGAGGTGCTGCTGACGCCCCCAACCCCAC\n+TGCCCCCTCCCTCCCCACCACCCACAGCCTCGGACAGGGGCCTGGCTACCCCATCCCCCT\n+CCCCATGCCCAGTCCCACGCCCCCTGGCAGCGCTCAAA\n+>Locus_7_Transcript_1/2_Confidence_0.667_Length_226\n+GCCCATCGCAGCACCAATGCCCAGGGCAGCCATTGGAAACAGAGGCGGAAATTCCTGCCC\n+GATGACATTGGCCAGTCACCCATTGTCTCCATGCCGGACGGAGACAAGGTGGACCTGGAA\n+GCCTTCAGCGAGTTTACCAAGATCATCACCCCGGCCATCACCCGTGTGGTGGACTTTGCC\n+AAAAAACTGCCCATGTTCTCCGAGTGTGGAGAAAAGAGAGAGAAAG\n+>Locus_7_Transcript_2/2_Confidence_0.667_Length_268\n+GCCCATCGCAGCACCAATGCCCAGGGCAGCCATTGGAAACAGAGGCGGAAATTCCTGCCC\n+GATGACATTGGCCAGTCACCCATTGTCTCCATGCCGGACGGAGACAAGGTGGACCTGGAA\n+GCCTTCAGCGAGTTTACCAAGATCATCACCCCGGCCATCACCCGTGTGGTGGACTTTGCC\n+AAAAAACTGCCCATGTTCTCCGAGCAATTTCGAGTGCAAGTGCCACAGTGTCAGCTAAAG\n+AAACACAACTGCGGGTTTTCTGCAGAGC\n+>Locus_8_Transcript_1/1_Confidence_1.000_Length_827\n+TGGGGTTGGCTTGAAACCAGCTTTGGGGGGTTCGATTCCTTCCTTTTTTGTCTAGATTTT\n+ATGTATACGGGTTCTTCGAATGTGTGGTAGGGTGGGGGGCATCCATATAGTCACTCCAGG\n+TTTATGGAGGGTTCTTCTACTATTAGGACTTTTCGCTTCGAAGCGAAGGCTTCTCAAATC\n+ATGAAAATTATTAATATTACTGCTGTTAGAGAAATGAATGAGCCTACAGATGATAGGATG\n+TTTCATGTGGTGTATGCATCGGGGTAGTCCGAGTAACGTCGGGGCATTCCGGATAGGCCG\n+AGAAAGTGTTGTGGGAAGAAAGTTAGATTTACGCCGATGAATATGATAGTGAAATGGATT\n+TTGGCGTAGGTTTGGTCTAGGGTGTAGCCTGAGAATAGGGGAAATCAGTGAATGAAGCCT\n+CCTATGATGGCAAATACAGCTCCTATTGATAGGAC'..b'TGGCTCCTGTGTTGTCAGCACAATTGATTACAGCTCCTACC\n+GGAAGACCCAAGGAAATCCGGAATTTCGCACCAGAGGACCCACCACGTCCTCGCTTCGA\n+>Locus_32_Transcript_1/1_Confidence_1.000_Length_180\n+CGGCCGCAGCCATGAGTATGCTCAGGCTTCAGAAGAGGCTCGCCTCTAGTGTCCTCCGCT\n+GTGGCAAGAAGAAGGTCTGGTTAGACCCCAATGAGACCAATGAAATCGCCAATGCCAACT\n+CCCGTCAGCAGATCCGGAAGCTCATCAAAGATGGGCTGATCATCCGCAAGCCTGTGACGG\n+>Locus_33_Transcript_1/1_Confidence_1.000_Length_127\n+ACTCCTGCTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCC\n+TCCCTTAGCAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTT\n+ACACCTA\n+>Locus_35_Transcript_1/1_Confidence_1.000_Length_307\n+CCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCT\n+CATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAA\n+ACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCT\n+AACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGG\n+ATTCTACCCTAGCATCACACACCGCACAATCCCCTATCTAGGCCTTCTTACCACAAGGCA\n+CACCTAC\n+>Locus_36_Transcript_1/1_Confidence_1.000_Length_246\n+CTTGTTTTATTTTAATGGCTGATCTATGTAATCACAGAGGCCAGTATGTACAGACAAAGT\n+GGGAGGTTTTATTTCTTGGTCTCTTCCTCCTTGGATAAAGTCTTGATGATCTCCTCCTTC\n+TTGGCCTGGAGGCGCTCTTCACGGCGCTTGCGTGCTTCCTTGGTCTTAGACCTGCGGGCC\n+TCAGCCTGGTCAGCCAGGAGCTTCTTGCGGGCCTTGTCTGCCTTCAGCTTGTGGATGTGT\n+TCCATG\n+>Locus_37_Transcript_1/1_Confidence_1.000_Length_172\n+TCTCACTGTGGGTTCTGAGGAAACTCTCAGGGGAAGACAGCTCTTCATACCCTCACATAA\n+CCCCACCCACACACAGGCCCAGAGACACCTACAGACACACCCCCGCCCCATCTCTCACAC\n+TCACACTCACACACTTGCGTGTCAGACACCTGCAGACATACATGCTCCTGCC\n+>Locus_38_Transcript_1/1_Confidence_1.000_Length_212\n+ACGGGATGGATCCAGGATGTAGTCTGTGTTACATGATTGATGAAGTACTTGATTCCATCT\n+GCTGTGTAAGCTTCCTCCCACCCATAAGGTAAACCCTCGGTTTCCCCCTGAGCTTTCATC\n+CTGAAGGCGAGGAGAAGCTAGATCCGCCACAAAAGGATAAGCCCTTCCCCACCACTAACG\n+GAGGAAACAAGTTGGCTCGGGATCCCGGGACG\n+>Locus_40_Transcript_1/1_Confidence_1.000_Length_132\n+CCCTGGGCAATGACGTCTTCAATGTTTTTTCCATTCAGCTCACTGATAACCTTGTTGAGC\n+CGGTCGTCGTCCGCCTCGATACCCACGCTGTCCAAGATCTTCTTGATGTCCTTGGCGCTG\n+GGGGAGGAGTTG\n+>Locus_41_Transcript_1/1_Confidence_1.000_Length_194\n+TAGGATCCTCTACGCACAACGCCTGCTCGCCTCCTCCGTGTGGTTGCCAAGCCAAGCCGC\n+CTGCTACCTTCATCACCAAATTGCACTCGCTCCTTCCTGGAATCCTTTTTCCTAGCTTCA\n+CCACCAAATCGTTAGCGCTCCTTCCTTCTTCCTAGCTTCCTTCACCAAATCGCACTGGCT\n+CCTGGACTCTTTTC\n+>Locus_43_Transcript_1/1_Confidence_1.000_Length_109\n+TGGAATTAAGGGTGTTAGTCATGTTAGCTTGTTTCAGGTGCGAGATAGTAGTAGGGTCGT\n+GGTGCTGGAGTTTAAGTTGAGTAGTAGGAATGCGGTAGTAGTTAGGATA\n+>Locus_44_Transcript_1/1_Confidence_1.000_Length_339\n+GGGTGTGAGCCCGGCCCGTGGCGGCCACGTCTCCCGGGAGATGCTGTGACGGACCCGCAC\n+GGGAGGAGCTCGCGCCTGGCCTGGCGACCCGGTGGACTCGGCCCGCGGCGGCGCGCTCAC\n+CCGCCCCGTTCAGATAAAGGCTGGTGGTGGGAGAATGCTATCGCTGCCCTGTTTCGGAGA\n+CACATTCCCGTCAGCTGGCTGATCCGCGCTACCCTGAGTGAGTCGGAAAACTTCGAAGCA\n+GCTGTTGGCAAGTTGGCCAAGACTCCCCTTATTGCTGATGTTTATTACATTGTTGGTGGC\n+ACGTCCCCCCGGGAGGGGGTGGTCATCACGAGGAACAGA\n+>Locus_45_Transcript_1/1_Confidence_1.000_Length_121\n+AGACCCTATGGAGCTTTAATTTATTAATGCAAGCAGTACCTAACAAACCCACAGGTCCTA\n+AACTACCAAACCTGCATTAAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTC\n+C\n+>Locus_46_Transcript_1/1_Confidence_1.000_Length_122\n+GGTCTTCTCGTCTTGCTGTGTCATGCCCGCCTCTTCACGGGCAGGTCAATTTCACTGGTT\n+AAAAGTAAGAGACAGCTGAACCCTCGTGGAGCCATTCATACAGGTCCCTATTTAAGGAAC\n+AA\n+>Locus_47_Transcript_1/1_Confidence_1.000_Length_156\n+GGGCACTCTCTGCCTGGGTCCGTTCTTCTTCCCTCTGGGCCTGGATGGCCTCCATTTCTG\n+TCTGCTGCTCCTTTAGCCTCATTTCCAGCTCCATTTTTTCCCTTTCTAAGCTCTCCAGAG\n+CCTTTGCCAGCTCCTGCTGGTGCCAGGAGCGCTCCT\n+>Locus_48_Transcript_1/1_Confidence_1.000_Length_185\n+GTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCT\n+ATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGAC\n+CCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCAA\n+AATAG\n+>Locus_50_Transcript_1/1_Confidence_1.000_Length_125\n+TCCGAACCCCCTCATGATTCTCGATTTTGCTGATAATCTTGATGTTCTTTCCCTTCTCTC\n+CCAGGACCTTCCTAACTTCATGGACATCAGATGCCTTGCGGATGAATGACGCAAACACCA\n+TATCA\n+>Locus_51_Transcript_1/1_Confidence_1.000_Length_187\n+GTCCACGCTTTCTGCCTTCTGCTCCACAGTGTCCTCAGGGAAGTGCGCGAATGTCACGGG\n+ACTGTTCTCTGTGGTTCCATAAGCAACCTTAGCTGCTGTACAAGCTCCGGACAGCTCACA\n+GGATTCTCCCCATGGTGAGCCACTTTTACATCACAAAGCTGTCCTGCAGGATCTAACTGC\n+ACTTCCA\n' 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| diff -r 000000000000 -r 966ea55e1aae tool-data/ctat_genome_resource_libs.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/ctat_genome_resource_libs.loc.sample Tue Jul 17 11:52:28 2018 -0400 |
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| @@ -0,0 +1,15 @@ +# This file lists the locations of CTAT Genome Resource Libraries +# Usually there will only be one library, but it is concievable +# that there could be multiple libraries. +# This file format is as follows +# (white space characters are TAB characters): +# +#<value> <name> <path> +# value is a unique id +# name is the display name +# path is the directory where the genome resource lib files are stored +# +#ctat_genome_resource_libs.loc could look like: +# +#GRCh38_v27_CTAT_lib_Feb092018 CTAT_GenomeResourceLib_GRCh38_v27_CTAT_lib_Feb092018 /path/to/ctat/genome/resource/lib/directory +# |
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| diff -r 000000000000 -r 966ea55e1aae tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Jul 17 11:52:28 2018 -0400 |
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| @@ -0,0 +1,14 @@ +<tables> + <table name="ctat_genome_resource_libs" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, path</columns> + <file path="tool-data/ctat_genome_resource_libs.loc" /> + </table> + <table name="ctat_centrifuge_indexes" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, path</columns> + <file path="tool-data/ctat_centrifuge_indexes.loc" /> + </table> + <table name="ctat_lncrna_annotations" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, path</columns> + <file path="tool-data/ctat_lncrna_annotations.loc" /> + </table> +</tables> |