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Commit message:
Upload ctat tools. |
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added:
ctat_metagenomics.xml test-data/centrifuge/SRR2219890_1_20k_reads.classification.report.txt test-data/centrifuge/SRR2219890_1_20k_reads.kraken_style_report.txt test-data/centrifuge/SRR2219890_1_adj_20k_reads.fastq tool-data/ctat_centrifuge_indexes.loc.sample tool_data_table_conf.xml.sample |
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| diff -r 000000000000 -r f92fcdde48fc ctat_metagenomics.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_metagenomics.xml Tue Jul 17 11:47:13 2018 -0400 |
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| @@ -0,0 +1,109 @@ +<tool id="ctat_metagenomics" name="ctat_metagenomics" version="1.0.0" profile="17.05"> + + <description>Centrifuge classifier for metagenomic sequences (RNA-Seq)</description> + <requirements> + <requirement type="package" version="1.0.3=py27pl5.22.0_2">centrifuge</requirement> + <requirement type="package" version="1.0.1">ctat-metagenomics</requirement> + </requirements> + <command detect_errors="default"> + <![CDATA[ + metagenomics + + --index "${index.fields.path}" + --out_dir "centrifuge" + + #if $format_type.format == "fasta" + --format fasta --unpaired_reads $format_type.fasta_file + #end if + + #if $format_type.format == "fastq" + --format fastq + #if $format_type.read_type.type == "single" + --read_type "single" --unpaired_reads $format_type.read_type.left_fq_single + #end if + + #if $format_type.read_type.type == "paired" + --read_type "paired" --left_fq $format_type.read_type.left_fq --right_fq $format_type.read_type.right_fq + #end if + #end if + + --threads 4 + ]]> + </command> + <stdio> + <exit_code range="1:" level="fatal" description="Error running centrifuge" /> + </stdio> + + <inputs> + + <conditional name="format_type"> + <param name= "format" type="select" label="Choose input format" help="Choose fasta for Trinity assembled reads"> + <option value="fasta" selected="true">FASTA</option> + <option value="fastq" selected="false">FASTQ</option> + </param> + <when value="fasta"> + <param name="fasta_file" type="data" format="fasta" label="Fasta file:" help="Trinity assembled reads in fasta format"/> + </when> + <when value="fastq"> + <conditional name="read_type"> + <param name= "type" type="select" label="Choose read type" help="Choose read type"> + <option value="single" selected="true">SINGLE END DATA</option> + <option value="paired" selected="false">PAIRED END DATA</option> + </param> + <when value="single"> + <param name="left_fq_single" type="data" format="fastq" label="Left_fq:" help="Left fastq"/> + </when> + <when value="paired"> + <param name="left_fq" type="data" format="fastq" label="Left_fq:" help="Left fastq"/> + <param name="right_fq" type="data" format="fastq" label="Right_fq:" help="Right fastq"/> + </when> + </conditional> + </when> + </conditional> + + <param name="index" type="select" label="Choose reference genome index :" help="Select genome index"> + <options from_data_table="ctat_centrifuge_indexes" /> + </param> + + </inputs> + + <outputs> + <data format="txt" name="classification_results" label="Centrifuge classification output" from_work_dir="centrifuge/classification.results.txt"/> + <data format="txt" name="classification_report" label="Centrifuge summary output" from_work_dir="centrifuge/classification.report.txt"/> + <data format="txt" name="kraken_style_report" label="Kraken-style report" from_work_dir="centrifuge/kraken_style_report.txt"/> + </outputs> + + <tests> + <test> + <!-- The following test uses one file that is unpaired reads. + --> + <param name="format" value="fastq" /> + <param name="type" value="single" /> + <param name="left_fq_single" value="centrifuge/SRR2219890_1.adj.fastq" /> + <param name="index" value="/N/dc2/projects/galaxyshared/trinity/dev/Trinity_CTAT/metagenomics/phv" /> + <output name="classification_results" > + <assert_contents> + <has_line_matching expression=".+" /> + <has_line line="readID	seqID	taxID	score	2ndBestScore	hitLength	queryLength	numMatches" /> + </assert_contents> + </output> + <output name="classification_report" file="centrifuge/SRR2219890_1.classification.report.txt" /> + <output name="kraken_style_report" file="centrifuge/SRR2219890_1.kraken_style_report.txt" /> + </test> + </tests> + + <help> +.. class:: infomark + +ctat_metagenomics is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). CTAT's metagenomics is a classifier for metagenomic sequences (RNA-Seq) for foreign transcript detection. It leverages Centrifuge, a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species, and Kraken. As well, we are leveraging RNA-Seq reads and Trinity-reconstructed transcripts. Our efforts here are being carried out in collaboration with the group of Steven Salzberg at JHU. + +For more information: + +https://ccb.jhu.edu/software/centrifuge/manual.shtml#what-is-centrifuge + + </help> +<citations> + <citation type="doi">10.1101/gr.210641.116</citation> +</citations> +</tool> + |
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| diff -r 000000000000 -r f92fcdde48fc test-data/centrifuge/SRR2219890_1_20k_reads.classification.report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/centrifuge/SRR2219890_1_20k_reads.classification.report.txt Tue Jul 17 11:47:13 2018 -0400 |
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| @@ -0,0 +1,8 @@ +name taxID taxRank genomeSize numReads numUniqueReads abundance +root 1 no rank 0 370 370 0.0 +Bacillus 1386 genus 5402033 31 31 0.0 +Homo sapiens 9606 species 3238442024 4384 4384 0.00519472 +synthetic construct 32630 species 26537524 8 8 0.000787552 +Methanocaldococcus 196118 genus 1584277 1 1 0.0 +Methanocaldococcus jannaschii DSM 2661 243232 leaf 1739927 50 50 0.994018 +Leptotrichia buccalis C-1013-b 523794 leaf 2465610 1 1 0.0 |
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| diff -r 000000000000 -r f92fcdde48fc test-data/centrifuge/SRR2219890_1_20k_reads.kraken_style_report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/centrifuge/SRR2219890_1_20k_reads.kraken_style_report.txt Tue Jul 17 11:47:13 2018 -0400 |
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| @@ -0,0 +1,58 @@ + 2.67 133 133 U 0 unclassified + 97.33 4845 370 - 1 root + 89.73 4467 0 - 131567 cellular organisms + 88.07 4384 0 D 2759 Eukaryota + 88.07 4384 0 - 33154 Opisthokonta + 88.07 4384 0 K 33208 Metazoa + 88.07 4384 0 - 6072 Eumetazoa + 88.07 4384 0 - 33213 Bilateria + 88.07 4384 0 - 33511 Deuterostomia + 88.07 4384 0 P 7711 Chordata + 88.07 4384 0 - 89593 Craniata + 88.07 4384 0 - 7742 Vertebrata + 88.07 4384 0 - 7776 Gnathostomata + 88.07 4384 0 - 117570 Teleostomi + 88.07 4384 0 - 117571 Euteleostomi + 88.07 4384 0 - 8287 Sarcopterygii + 88.07 4384 0 - 1338369 Dipnotetrapodomorpha + 88.07 4384 0 - 32523 Tetrapoda + 88.07 4384 0 - 32524 Amniota + 88.07 4384 0 C 40674 Mammalia + 88.07 4384 0 - 32525 Theria + 88.07 4384 0 - 9347 Eutheria + 88.07 4384 0 - 1437010 Boreoeutheria + 88.07 4384 0 - 314146 Euarchontoglires + 88.07 4384 0 O 9443 Primates + 88.07 4384 0 - 376913 Haplorrhini + 88.07 4384 0 - 314293 Simiiformes + 88.07 4384 0 - 9526 Catarrhini + 88.07 4384 0 - 314295 Hominoidea + 88.07 4384 0 F 9604 Hominidae + 88.07 4384 0 - 207598 Homininae + 88.07 4384 0 G 9605 Homo + 88.07 4384 4384 S 9606 Homo sapiens + 1.02 51 0 D 2157 Archaea + 1.02 51 0 P 28890 Euryarchaeota + 1.02 51 0 C 183939 Methanococci + 1.02 51 0 O 2182 Methanococcales + 1.02 51 0 F 196117 Methanocaldococcaceae + 1.02 51 1 G 196118 Methanocaldococcus + 1.00 50 0 S 2190 Methanocaldococcus jannaschii + 1.00 50 50 - 243232 Methanocaldococcus jannaschii DSM 2661 + 0.64 32 0 D 2 Bacteria + 0.62 31 0 - 1783272 Terrabacteria group + 0.62 31 0 P 1239 Firmicutes + 0.62 31 0 C 91061 Bacilli + 0.62 31 0 O 1385 Bacillales + 0.62 31 0 F 186817 Bacillaceae + 0.62 31 31 G 1386 Bacillus + 0.02 1 0 P 32066 Fusobacteria + 0.02 1 0 C 203490 Fusobacteriia + 0.02 1 0 O 203491 Fusobacteriales + 0.02 1 0 F 1129771 Leptotrichiaceae + 0.02 1 0 G 32067 Leptotrichia + 0.02 1 0 S 40542 Leptotrichia buccalis + 0.02 1 1 - 523794 Leptotrichia buccalis C-1013-b + 0.16 8 0 - 28384 other sequences + 0.16 8 0 - 81077 artificial sequences + 0.16 8 8 S 32630 synthetic construct |
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| diff -r 000000000000 -r f92fcdde48fc test-data/centrifuge/SRR2219890_1_adj_20k_reads.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/centrifuge/SRR2219890_1_adj_20k_reads.fastq Tue Jul 17 11:47:13 2018 -0400 |
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| b'@@ -0,0 +1,20000 @@\n+@HWI-D00361:29:H8HM6ADXX:1:1101:1238:2179/1\n+CGCTCCCCTGACACGTAGGCNNNCATACTGATGCGGTATTGTGCCAGCAT\n++SRR2219890.1 HWI-D00361:29:H8HM6ADXX:1:1101:1238:2179\n+<<<BBBBBBBBBBBBBBBBB###0<BBBBBBBBBBB<BBBBBBBBBBBBB\n+@HWI-D00361:29:H8HM6ADXX:1:1101:1320:2201/1\n+GGGTCGGGAGGAACGGGGGGCGGGAAAGATCCGCCGGGCCGCCGACACGG\n++SRR2219890.2 HWI-D00361:29:H8HM6ADXX:1:1101:1320:2201\n+BBBFFFFFFFFFFIIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@HWI-D00361:29:H8HM6ADXX:1:1101:1956:2153/1\n+CTCTTGATGGACNNNNNNNNNNNNNNNNNNNNNCTGCATATGAAACCCCG\n++SRR2219890.3 HWI-D00361:29:H8HM6ADXX:1:1101:1956:2153\n+<<<BBBBBBBBB#####################00<<BBBB<BBBBBBBB\n+@HWI-D00361:29:H8HM6ADXX:1:1101:1766:2210/1\n+CTCAATCAGGCCCATCACCCTCTGGAAGTGCCGGGCACTAATGATTCTTC\n++SRR2219890.4 HWI-D00361:29:H8HM6ADXX:1:1101:1766:2210\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIII\n+@HWI-D00361:29:H8HM6ADXX:1:1101:2091:2150/1\n+CTAGAAAGGATANNNNNNNNNNNNNNNNNNNNNNANTGTGANGTGGAACN\n++SRR2219890.5 HWI-D00361:29:H8HM6ADXX:1:1101:2091:2150\n+<<<BBBBBBBBB######################################\n+@HWI-D00361:29:H8HM6ADXX:1:1101:2204:2207/1\n+CCTGGATATGGAGCAAAAGACCCTCCAATACTTTCCCAGCCCTCAGAAAG\n++SRR2219890.6 HWI-D00361:29:H8HM6ADXX:1:1101:2204:2207\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIII\n+@HWI-D00361:29:H8HM6ADXX:1:1101:2287:2213/1\n+ACCAGATATATAATTTATTATGTTGCTTATGCATTGTACACTGTAACTCC\n++SRR2219890.7 HWI-D00361:29:H8HM6ADXX:1:1101:2287:2213\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIII\n+@HWI-D00361:29:H8HM6ADXX:1:1101:2785:2170/1\n+GTCCAGATTCCGGGCACTNNNNNGTNCCCTCTATCACTTCCACCTCCAGC\n++SRR2219890.8 HWI-D00361:29:H8HM6ADXX:1:1101:2785:2170\n+##################################################\n+@HWI-D00361:29:H8HM6ADXX:1:1101:3508:2207/1\n+CCCAACTCTGCTGCCCTTGCTGCTGGGCAGTGCCTGTCCTAAGAGGGGAC\n++SRR2219890.9 HWI-D00361:29:H8HM6ADXX:1:1101:3508:2207\n+BBBFFFFFFFFFFIIIIIFFFFFFIIIIFIIIFIIIBFFIIIFFFIFIII\n+@HWI-D00361:29:H8HM6ADXX:1:1101:3553:2220/1\n+CTTAGTAAATATAAAACTTAAGCTACTTGAACACTGGGGCTTATAAAGTG\n++SRR2219890.10 HWI-D00361:29:H8HM6ADXX:1:1101:3553:2220\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFF\n+@HWI-D00361:29:H8HM6ADXX:1:1101:3940:2186/1\n+CTTCCTCCCTACCAATTTTTAAGCTAACTCAGATTTACTCTCACTTCTCT\n++SRR2219890.11 HWI-D00361:29:H8HM6ADXX:1:1101:3940:2186\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-D00361:29:H8HM6ADXX:1:1101:4856:2179/1\n+CTCTCCTGTTCTCTGGTGACNNCCCACTTCCCACTCCCCCACCTCTGTCC\n++SRR2219890.12 HWI-D00361:29:H8HM6ADXX:1:1101:4856:2179\n+<<<BBBBBBBBBBBBB<BBB##00BBBB<BBBBBBBBBBBBB<BBBBBB<\n+@HWI-D00361:29:H8HM6ADXX:1:1101:4825:2232/1\n+CATTAGAAGAACATAAATCAGATACTTTGTTTTGACCTTCTGCCAGTTCC\n++SRR2219890.13 HWI-D00361:29:H8HM6ADXX:1:1101:4825:2232\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-D00361:29:H8HM6ADXX:1:1101:5435:2211/1\n+GGCTCACGCTGACCTCTGTCCGCGTGGGAGGGGCCGGTGTGAGGCAAGGG\n++SRR2219890.14 HWI-D00361:29:H8HM6ADXX:1:1101:5435:2211\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIFFBFFFFFFFFFF\n+@HWI-D00361:29:H8HM6ADXX:1:1101:5338:2249/1\n+CACAAAAAAGACATTTTCTTTTGCAAATCAAAACAGGAAAGAAAGGAAAA\n++SRR2219890.15 HWI-D00361:29:H8HM6ADXX:1:1101:5338:2249\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-D00361:29:H8HM6ADXX:1:1101:6214:2155/1\n+CTGGAGAGCCCCNNNNNNNNNNNNNNNNNNNNNCCCGGAGGGGCCATCCA\n++SRR2219890.16 HWI-D00361:29:H8HM6ADXX:1:1101:6214:2155\n+<<<BBBBBBBBB#####################00<BBBBBBBBBBBBB<\n+@HWI-D00361:29:H8HM6ADXX:1:1101:6096:2166/1\n+TGTCTTTCCACATCAGANNNNNNNNNNNGAGAGGTGTCAAAAGTCTGTTT\n++SRR2219890.17 HWI-D00361:29:H8HM6ADXX:1:1101:6096:2166\n+<<<BBBBBBBBBBBBBB###########00<BBB<BBBBBBBBBBBBBBB\n+@HWI-D00361:29:H8HM6ADXX:1:1101:6278:2191/1\n+CCGGGGGGATTTTTGGCCTAAACTGAAAATGAAACCGGGTAAAGGCGCCT\n++SRR2219890.18 HWI-D00361:29:H8HM6ADXX:1:1101:6278:2191\n+BBBFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<BFFFFBFFFF\n+@HWI-D00361:29:H8HM6ADXX:1:1101:6579:2234/1\n+GTCGTGCACAGCTGTCAGAGTACGGCTCCTGGGACGCTTTTGCTTATTTT\n++SRR2219890.19 HWI-D00361:29:H8HM6ADXX:1:1101:6579:2234\n+BBBFFFFFFFFFFIIIIIIIFFIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-D00361:29:H8HM6ADXX:1:1101:6891:2200/1\n+GCCCTTTTTAACAGGAAGGCGGAGTGTG'..b'IIIIIIII\n+@HWI-D00361:29:H8HM6ADXX:1:1101:14467:9091/1\n+CTGTAGTATTCTCCTAGCATGTGCTGAAGATATTTCTGTAGACCTATTAC\n++SRR2219890.4982 HWI-D00361:29:H8HM6ADXX:1:1101:14467:9091\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-D00361:29:H8HM6ADXX:1:1101:14652:9066/1\n+GCCTGTTTTACTGCTGCCGCTGCTAGATTTGCCAGATGATTTTGAAGAGA\n++SRR2219890.4983 HWI-D00361:29:H8HM6ADXX:1:1101:14652:9066\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIII\n+@HWI-D00361:29:H8HM6ADXX:1:1101:14692:9100/1\n+GGCCTGGGTACGTTTGGGAGCCTGAGCTGGAACTGAAGCTGGGGCTGCAG\n++SRR2219890.4984 HWI-D00361:29:H8HM6ADXX:1:1101:14692:9100\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-D00361:29:H8HM6ADXX:1:1101:14513:9171/1\n+GGTTGCTGACCCAGCCCCAGCCTCGGCTTTCTTGTCGGCACCAGGTGGCA\n++SRR2219890.4985 HWI-D00361:29:H8HM6ADXX:1:1101:14513:9171\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIBFFII\n+@HWI-D00361:29:H8HM6ADXX:1:1101:14770:9069/1\n+CAGTAAAATTGTAATAAGCAGTGCTTGAATTATTTGGTTTCGGTTGTTTT\n++SRR2219890.4986 HWI-D00361:29:H8HM6ADXX:1:1101:14770:9069\n+BBBFFFFFFFFFFIIIIIIIIFFFIIIIIIIIIIIIIFIIIIIFIIIIII\n+@HWI-D00361:29:H8HM6ADXX:1:1101:14798:9078/1\n+CACCCGCTTTGGGCTGCATTCCCAAGCAACCCGACTCCGGGAAGACCCGG\n++SRR2219890.4987 HWI-D00361:29:H8HM6ADXX:1:1101:14798:9078\n+BBBFFFFFFFFFFFIFFFFIFFFFFFIIIIIFFIIIFFFIIIIIFIFFFF\n+@HWI-D00361:29:H8HM6ADXX:1:1101:14758:9136/1\n+GCCTTTCTGGAAATGAGATGGGAGCTGGCCTTGGGGTTGAAGGAAGGATC\n++SRR2219890.4988 HWI-D00361:29:H8HM6ADXX:1:1101:14758:9136\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFII\n+@HWI-D00361:29:H8HM6ADXX:1:1101:14974:9210/1\n+GCTCCCGCGAGTCACTCACCTTGTTTTGCGAGGAGGCCGCAGGCGGAGGT\n++SRR2219890.4989 HWI-D00361:29:H8HM6ADXX:1:1101:14974:9210\n+BBBFFFFFFFFFFFIIIFIIIFIIIIIIFIIIIFFBFIIFFFFFFBBBF7\n+@HWI-D00361:29:H8HM6ADXX:1:1101:15174:9060/1\n+CTCAAATGTCACTACTGCGTGTCTCTGGGTGGTACGATTCTAGGTGATAT\n++SRR2219890.4990 HWI-D00361:29:H8HM6ADXX:1:1101:15174:9060\n+BBBFFFFFFFFFFIIIIIIIIFIIIIIIIFFIFFIIIIIIIIIIFFIIII\n+@HWI-D00361:29:H8HM6ADXX:1:1101:15041:9186/1\n+GGGGAGACGAAGTGGAAGGGGGTACAAGGGGAGTTTCTGGGGTGATGGAA\n++SRR2219890.4991 HWI-D00361:29:H8HM6ADXX:1:1101:15041:9186\n+BBBFFFFFFFFFFFIIIIIIIIBFIIIIIIIBFFIIIIIIIF7<FFFFFF\n+@HWI-D00361:29:H8HM6ADXX:1:1101:15361:9047/1\n+CCGAGAAAGTGTTGTGGGAAGAAAGTTAGATTTACGCCGATGAATATGAT\n++SRR2219890.4992 HWI-D00361:29:H8HM6ADXX:1:1101:15361:9047\n+BBBFFFFFFFFFFIFFIIIIIIIIIFFIIIIIIIIIIIIFFIIIIIIIII\n+@HWI-D00361:29:H8HM6ADXX:1:1101:15402:9123/1\n+CGACTCCCTTTCGATCGGCCGAGGGCAACGGAGGCCATCGCCCGTCCCTT\n++SRR2219890.4993 HWI-D00361:29:H8HM6ADXX:1:1101:15402:9123\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFBFFFFF\n+@HWI-D00361:29:H8HM6ADXX:1:1101:15303:9222/1\n+CATGCTGGGTGCCTGGGAAGTATGTACACGGGGTACGTGCCAAGCATCCT\n++SRR2219890.4994 HWI-D00361:29:H8HM6ADXX:1:1101:15303:9222\n+BBBFFFFFFFFFFIIIIIIIFIIIFIIIIIIIIFFIIIIIIIIIIIIIII\n+@HWI-D00361:29:H8HM6ADXX:1:1101:15537:9127/1\n+GTCTGCAGCGCACATAGCATCAGGTTCTGCAGCTCCAGGGTCTCCACCAG\n++SRR2219890.4995 HWI-D00361:29:H8HM6ADXX:1:1101:15537:9127\n+BBBFFFFFFFFFFIIIIIIIIIIIFIIIIIIIIIIIIIIIFFIIIIIIII\n+@HWI-D00361:29:H8HM6ADXX:1:1101:15792:9027/1\n+TGTTAAGATCCAAACACTCAGCACAATGCTTAAAAAACAAAAAAACAAAC\n++SRR2219890.4996 HWI-D00361:29:H8HM6ADXX:1:1101:15792:9027\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-D00361:29:H8HM6ADXX:1:1101:16203:9037/1\n+GCTAGTTTAACATAATTGGCTGATTTTATACAGCACTTATATCTTTTAGT\n++SRR2219890.4997 HWI-D00361:29:H8HM6ADXX:1:1101:16203:9037\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIF\n+@HWI-D00361:29:H8HM6ADXX:1:1101:16060:9043/1\n+CCTGCTCCTGTTCCAACATCATCTTCTCTCAGTTCCTCTGGTCGGCTGAC\n++SRR2219890.4998 HWI-D00361:29:H8HM6ADXX:1:1101:16060:9043\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFIIIIIII\n+@HWI-D00361:29:H8HM6ADXX:1:1101:16352:9007/1\n+GGTCTCATAGTAGCGTGTCCACTGAGCCATGGTCATTTCAATGCCTTTCT\n++SRR2219890.4999 HWI-D00361:29:H8HM6ADXX:1:1101:16352:9007\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIII\n+@HWI-D00361:29:H8HM6ADXX:1:1101:16743:9055/1\n+GTTTGTAATAGGAAATCATGTCATCCAGAGTTTTGAAAGTAACTGTGGGG\n++SRR2219890.5000 HWI-D00361:29:H8HM6ADXX:1:1101:16743:9055\n+BBBFFFFFFFFFFFFIIIIIFFIIIIIIFFFIFIIIFIIFFIFIIBFFII\n' |
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| diff -r 000000000000 -r f92fcdde48fc tool-data/ctat_centrifuge_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/ctat_centrifuge_indexes.loc.sample Tue Jul 17 11:47:13 2018 -0400 |
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| @@ -0,0 +1,15 @@ +# This file lists the locations of CTAT Centrifuge Indexes +# Usually there will only be one index, but it is concievable +# that there could be multiple indexes. +# 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 index files are stored +# +#ctat_centrifuge_indexes.loc could look like: +# +#p_compressed+h+v CTAT_CentrifugeIndex_p_compressed+h+v /path/to/centrifuge/index/p_compressed+h+v +# |
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| diff -r 000000000000 -r f92fcdde48fc 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 11:47:13 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> |