| Next changeset 1:0fb894bd8eba (2015-07-21) |
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Commit message:
Uploaded |
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added:
cd_hit_dup.xml test-data/cd-hit-dup_in.fastqsanger test-data/cd-hit-dup_out.dup_clusters.tabular test-data/cd-hit-dup_out.fastqsanger test-data/cd-hit-dup_out_chimera.chimeric_clusters.tabular test-data/cd-hit-dup_out_chimera.dup_clusters.tabular test-data/cd-hit-dup_out_chimera.fastqsanger tool_dependencies.xml |
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| diff -r 000000000000 -r 2e150ed1b76e cd_hit_dup.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cd_hit_dup.xml Wed Apr 29 12:06:47 2015 -0400 |
| [ |
| b'@@ -0,0 +1,135 @@\n+<tool id="cd_hit_dup" name="cd-hit-dup" version="0.0.1">\n+ <requirements>\n+ <requirement type="package" version="0.5-2012-03-07-fix-dan-gh-0.0.1">cd-hit-auxtools</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" />\n+ <exit_code range=":-1" />\n+ </stdio>\n+\n+ <command><![CDATA[\n+ cd-hit-dup\n+ -i "${ fastq_input.fastq_input1 }"\n+ #if str( $fastq_input.fastq_input_selector ) == "paired":\n+ -i2 "${ fastq_input.fastq_input2 }"\n+ #elif str( $fastq_input.filter_chimeras.filter_chimeras_selector ) == "true":\n+ -f "true"\n+ -s "${ fastq_input.filter_chimeras.min_chimeric_length }"\n+ -a "${ fastq_input.filter_chimeras.abundance_cutoff }"\n+ -b "${ fastq_input.filter_chimeras.abundance_ratio }"\n+ -p "${ fastq_input.filter_chimeras.dissimilarity_control }"\n+ #end if\n+ -u "${ prefix_length }"\n+ -m "${ match_length }"\n+ #if str( $mismatches_allowed ) != "":\n+ #if float( str( $mismatches_allowed ) ) == int( float( str( $mismatches_allowed ) ) ):\n+ -e "${ int( float( str( $mismatches_allowed ) ) ) }"\n+ #else:\n+ -e "${ mismatches_allowed }"\n+ #end if\n+ #end if\n+ -d "${ description_length }"\n+ -o "output"\n+ ]]>\n+ </command>\n+ <inputs>\n+ <conditional name="fastq_input">\n+ <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="For joined Paired-end reads choose Single.">\n+ <option value="paired">Paired</option>\n+ <option value="single" selected="True">Single</option>\n+ </param>\n+ <when value="paired">\n+ <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>\n+ <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>\n+ </when>\n+ <when value="single">\n+ <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select read dataset" help="Specify dataset with single reads"/>\n+ <conditional name="filter_chimeras">\n+ <param name="filter_chimeras_selector" type="select" label="Filter out chimeric clusters">\n+ <option value="true">Yes</option>\n+ <option value="false" selected="True">No</option>\n+ </param>\n+ <when value="true">\n+ <param name="min_chimeric_length" type="integer" value="30" min="20" label="Minimum length of common sequence shared between a chimeric read and each of its parents" help="-s"/>\n+ <param name="abundance_cutoff" type="integer" value="1" min="1" label="Abundance cutoff" help="-a; Tool Author recommend default of 2, but this would require the chimera itself to need 2 copies"/>\n+ <param name="abundance_ratio" type="integer" value="1" min="1" label="Abundance ratio between a parent read and a chimeric read" help="-b"/>\n+ <param name="dissimilarity_control" type="integer" value="1" min="1" label="Dissimilarity control for chimeric filtering" help="-p"/>\n+ </when>\n+ <when value="false">\n+ <!-- do nothing here -->\n+ </when>\n+ </conditional>\n+ </when>\n+ </conditional>\n+ <param name="prefix_length" type="integer" value="0" min="0" label="Length of prefix to be used in the analysis" help="-u"/>\n+ <param name="match_length" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Match length" help="-m; specifies whether the lengths of two reads should be exact'..b'cates are removed.\n+\n+\n+ **Options**\n+\n+ +--------+-------------------------------------------------------------------------------------------------------------------+\n+ | Option | Description |\n+ +========+===================================================================================================================+\n+ |-i | Input file |\n+ +--------+-------------------------------------------------------------------------------------------------------------------+\n+ |-i2 | Second input file |\n+ +--------+-------------------------------------------------------------------------------------------------------------------+\n+ |-o | Output file |\n+ +--------+-------------------------------------------------------------------------------------------------------------------+\n+ |-d | Description length (default 0, truncate at the first whitespace character) |\n+ +--------+-------------------------------------------------------------------------------------------------------------------+\n+ |-u | Length of prefix to be used in the analysis (default 0, for full/maximum length) |\n+ +--------+-------------------------------------------------------------------------------------------------------------------+\n+ |-m | Match length (true/false, default true) |\n+ +--------+-------------------------------------------------------------------------------------------------------------------+\n+ |-e | Maximum number/percent of mismatches allowed |\n+ +--------+-------------------------------------------------------------------------------------------------------------------+\n+ |-f | Filter out chimeric clusters (true/false, default false) |\n+ +--------+-------------------------------------------------------------------------------------------------------------------+\n+ |-s | Minimum length of common sequence shared between a chimeric read and each of its parents (default 30, minimum 20) |\n+ +--------+-------------------------------------------------------------------------------------------------------------------+\n+ |-a | Abundance cutoff (default 1 without chimeric filtering, 2 with chimeric filtering) |\n+ +--------+-------------------------------------------------------------------------------------------------------------------+\n+ |-b | Abundance ratio between a parent read and a chimeric read (default 1) |\n+ +--------+-------------------------------------------------------------------------------------------------------------------+\n+ |-p | Dissimilarity control for chimeric filtering (default 1) |\n+ +--------+-------------------------------------------------------------------------------------------------------------------+\n+\n+\n+ ]]>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/bts565</citation>\n+ </citations>\n+</tool>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 2e150ed1b76e test-data/cd-hit-dup_in.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cd-hit-dup_in.fastqsanger Wed Apr 29 12:06:47 2015 -0400 |
| b |
| @@ -0,0 +1,28 @@ +@A +CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGCGGGATGGAGGCCTTCGGGTTGTAAACCGCTTTTGATCGGGAGCAAGCCCTTCGGGGTGAGTGTACCCTTCGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGCCCATCGCTTAACGGTGGGTCTGCGCCGGGTACGGGCGGGCTGGAGTGCGGTAGGGGAGACTGGAATTGCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCGCTGGGCCGTCACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCGGGTAGTA ++ +>AAAAAADADBBGGGGGGGGGGFGHHHHHGFHGHHHHHHGGGGEHFHHHHFHHHHGGEFFEFCGGGGGCGGGGGBCF?FHHHHGGHGGGHFHHHCDGGGHHFGHGGGGGGHHHEGEFHHH?DDDG.CGHBGFHHGGGG.;;.BFGFFGGAA?ABFB9FDAFEF/FFFAFFFFDAA.:FBBAB/AAE9ADFFFFDFBFFBFFFB;AF;FFF@EFFFBFFE>AEFFFFFE@B@@B-E@A?DFA-AACF/CAFFAB9------FFA9BAFBA-FEA9;@@A9-.C;9-A-@A@;AEF;FHHCCC@@<GEHGHHHGF111GF<>--//?G?1F/?</HGDG>GF1G>HGHGB/B//GG2F2GE??>111F/GCGHGEF0BEE>//0//E>///F12HFGGGGHGHHGAGCGGHGGEEEE0GGGHGGGGHHGGGGGBGGGF?ADDAFFFAA>11 +@A2 +CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGCGGGATGGAGGCCTTCGGGTTGTAAACCGCTTTTGATCGGGAGCAAGCCCTTCGGGGTGAGTGTACCCTTCGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGCCCATCGCTTAACGGTGGGTCTGCGCCGGGTACGGGCGGGCTGGAGTGCGGTAGGGGAGACTGGAATTGCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCGCTGGGCCGTCACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCGGGTAGTA ++ +>AAAAAADADBBGGGGGGGGGGFGHHHHHGFHGHHHHHHGGGGEHFHHHHFHHHHGGEFFEFCGGGGGCGGGGGBCF?FHHHHGGHGGGHFHHHCDGGGHHFGHGGGGGGHHHEGEFHHH?DDDG.CGHBGFHHGGGG.;;.BFGFFGGAA?ABFB9FDAFEF/FFFAFFFFDAA.:FBBAB/AAE9ADFFFFDFBFFBFFFB;AF;FFF@EFFFBFFE>AEFFFFFE@B@@B-E@A?DFA-AACF/CAFFAB9------FFA9BAFBA-FEA9;@@A9-.C;9-A-@A@;AEF;FHHCCC@@<GEHGHHHGF111GF<>--//?G?1F/?</HGDG>GF1G>HGHGB/B//GG2F2GE??>111F/GCGHGEF0BEE>//0//E>///F12HFGGGGHGHHGAGCGGHGGEEEE0GGGHGGGGHHGGGGGBGGGF?ADDAFFFAA>11 +@B +CCTACGGGCGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAAGGACGACGTATTTCGGTATGTAAACTTCTATCAGCAAGGAAGATGATGACGGTACTTGACTAAGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGGCGGCCATGCAAGTCAGAAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTTGAAACTGTAAGGCTAGATTGCCGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTGAATGACGCTGAGGCTCGGAAGCGTGGGGAGCAAACAGGATTAGATACCCCAGTAGTA ++ +>>AAAA>DBBBBEGGGGGGGGGGGHHHHHHHHHHHHHHGGGGHHHGHHHHHHHHHGGGGGGGGGGGGGGHHHGGGGDHHHHHHGGHGHHHHHHHHHHHHHHHHFHHGHHHHHHHHHHHGGGHGHHHHHHHHHHHHHHFGGGGGGGGGFGGGGGGGGGGGGGBBBBFFFFFFFFFFFFFBBBFFFFFFFFFFFFFFFFFFFFFFBDBFFFFFFFFFFFFBFFFFBFBFFFFFFFFFFFFFFFFGFFFFFGGGFFE@A@CCGCHGHGFFG/GD00HHGGDBCBHDCFFFG><-?C<?GHGHHHGGGGGHHGGGD1CF0FGBC/CCAGGFGGEE/GFGBHGF2F1BHFHHHHGHBGEFFGGGFEHGGEECFD12BGFGGGHGHGDFHHGGGGHGHHGGGGGGHGGFGGGHGGGHHFHHFHFGGGGCFGGGGADA@BFFAA>11 +@B2 +CCTACGGGCGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAAGGACGACGTATTTCGGTATGTAAACTTCTATCAGCAAGGAAGATGATGACGGTACTTGACTAAGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGGCGGCCATGCAAGTCAGAAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTTGAAACTGTAAGGCTAGATTGCCGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTGAATGACGCTGAGGCTCGGAAGCGTGGGGAGCAAACAGGATTAGATACCCCAGTAGTA ++ +>>AAAA>DBBBBEGGGGGGGGGGGHHHHHHHHHHHHHHGGGGHHHGHHHHHHHHHGGGGGGGGGGGGGGHHHGGGGDHHHHHHGGHGHHHHHHHHHHHHHHHHFHHGHHHHHHHHHHHGGGHGHHHHHHHHHHHHHHFGGGGGGGGGFGGGGGGGGGGGGGBBBBFFFFFFFFFFFFFBBBFFFFFFFFFFFFFFFFFFFFFFBDBFFFFFFFFFFFFBFFFFBFBFFFFFFFFFFFFFFFFGFFFFFGGGFFE@A@CCGCHGHGFFG/GD00HHGGDBCBHDCFFFG><-?C<?GHGHHHGGGGGHHGGGD1CF0FGBC/CCAGGFGGEE/GFGBHGF2F1BHFHHHHGHBGEFFGGGFEHGGEECFD12BGFGGGHGHGDFHHGGGGHGHHGGGGGGHGGFGGGHGGGHHFHHFHFGGGGCFGGGGADA@BFFAA>11 +@C +CCTACGGGCGGCTGCAGTGGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGAGTGATGACGGCCTTCGGGTTGTAAAGCTCTGTTAATCGGGACGAAAGGCCTTCTTGCGAATAGTGAGAAGGATTGACGGTACCGGAATAGAAAGCCACGGCTAGCTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGATAGGTCAGTCTGTCTTAAAAGTTCGGGGCTTAACCCCGTGATGGGATGGAAACTGCCAATCTAGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGACTTTCTGGACGAAAACTGACGCTGAGGCGCGAAAGCCAGGGGAGCGAACGGGATTAGATACCCGGGTAGTC ++ +ABBCCDCCCCCCGGGGGGGGGGGGHHHHHHGGGGGHHHHGGGGGHHHHHHGGGGGHHHGGGGGGGGGGHHHHHHHGGGGGHHHGGHGGGHHHHHHHHHHHHHHHGGGGGGGGGGHHHHHHHHHFG-DGGGGGGGGGGGGGGGFGGGGGGGGGGGFFFFFFFFFFFFFFFFFFBFFFFFFFHFFFFFFFFFFFFFFFHFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/B/FBFFGFBGFFGGGGFFAGGGGGGGFCGCDAGCGBHHHFFHHHHHGGGHFGD0HHHHHHGGGGGHHHHHHHHHEHHHHHFHHGHHHHHGGGGGHHHHHGGGGGHHHHHHHHGHHHHFHGHGFHHHGGGGHHGGGGGFGGHHHHGGGHGHHGHHGGGGGHHHGGGGGGGHHHHHHGGGGGHGGGHHHFFGGGGGGGGGBBBBFFFBBBA3 +@D +CCTACGGGTGGCTGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGGAGGCCTTCGGGTTGTAAACCTCTTTTGTTAGGGAGCAAGGCACTTTGTGTTGAGTGTACCTTTCGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGTCCATCGCTTAACGGTGGATCCGCGCCGGGTACGGGCGGGCTTGAGTGCGGTAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCGAGTAGTC ++ +DDDDDDDCCCCFGGGGGGGGGGGGHHHHHHHCHHHHHHHGGGGGHGHHHHHHHHHGGGGGGGGGGGGGHGGHGGGHGGGHHHHGGHGGGHGHHHHHHHHHHHHHHHHHGGHHHGHHHHHGHHHFGHHHHHHHHHHHHHGGFGGHHHFHHGGGGGHHHGGGGGGGFFGGGGGGADFFFEFFFFFFFDFBAFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFDFFFFFF@DFFFFFFFFFFFFFFFFFFFFBDA9.;FFFFFFFFFFFDC@??D9?-?GGGGGGGGFGHEFGGHHGGFCFHHGHFFHHHHHGHHHHGCGGGCFHHGGC?GHHHHGHHHHEHHHHEGEEDFHHHHHGHGHHGF1GGGGHHHHHF3FHFG1HGGGGGEFFHHGGGGGHHHHHGGFGFHGGFEGGGGGGHGGGHHHHFGGGGGGGGGBBBBFBFBBBBB +@chimeric_read +CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGCGGGATGGAGGCCTTCGGGTTGTAAACCGCTTTTGATCGGGAGCAAGCCCTTCGGGGTGAGTGTACCCTTCGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCCATGCAAGTCAGAAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTTGAAACTGTAAGGCTAGATTGCCGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTGAATGACGCTGAGGCTCGGAAGCGTGGGGAGCAAACAGGATTAGATACCCCAGTAGTA ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF |
| b |
| diff -r 000000000000 -r 2e150ed1b76e test-data/cd-hit-dup_out.dup_clusters.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cd-hit-dup_out.dup_clusters.tabular Wed Apr 29 12:06:47 2015 -0400 |
| b |
| @@ -0,0 +1,12 @@ +>Cluster 0 +0 465nt, >C... * +>Cluster 1 +0 450nt, >D... * +>Cluster 2 +0 449nt, >A... * +1 449nt, >A2... at 1:449:1:449/+/100.00% +>Cluster 3 +0 440nt, >B... * +1 440nt, >B2... at 1:440:1:440/+/100.00% +>Cluster 4 +0 440nt, >chimeric_read... * |
| b |
| diff -r 000000000000 -r 2e150ed1b76e test-data/cd-hit-dup_out.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cd-hit-dup_out.fastqsanger Wed Apr 29 12:06:47 2015 -0400 |
| b |
| @@ -0,0 +1,20 @@ +@C +CCTACGGGCGGCTGCAGTGGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGAGTGATGACGGCCTTCGGGTTGTAAAGCTCTGTTAATCGGGACGAAAGGCCTTCTTGCGAATAGTGAGAAGGATTGACGGTACCGGAATAGAAAGCCACGGCTAGCTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGATAGGTCAGTCTGTCTTAAAAGTTCGGGGCTTAACCCCGTGATGGGATGGAAACTGCCAATCTAGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGACTTTCTGGACGAAAACTGACGCTGAGGCGCGAAAGCCAGGGGAGCGAACGGGATTAGATACCCGGGTAGTC ++C +ABBCCDCCCCCCGGGGGGGGGGGGHHHHHHGGGGGHHHHGGGGGHHHHHHGGGGGHHHGGGGGGGGGGHHHHHHHGGGGGHHHGGHGGGHHHHHHHHHHHHHHHGGGGGGGGGGHHHHHHHHHFG-DGGGGGGGGGGGGGGGFGGGGGGGGGGGFFFFFFFFFFFFFFFFFFBFFFFFFFHFFFFFFFFFFFFFFFHFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/B/FBFFGFBGFFGGGGFFAGGGGGGGFCGCDAGCGBHHHFFHHHHHGGGHFGD0HHHHHHGGGGGHHHHHHHHHEHHHHHFHHGHHHHHGGGGGHHHHHGGGGGHHHHHHHHGHHHHFHGHGFHHHGGGGHHGGGGGFGGHHHHGGGHGHHGHHGGGGGHHHGGGGGGGHHHHHHGGGGGHGGGHHHFFGGGGGGGGGBBBBFFFBBBA3 +@D +CCTACGGGTGGCTGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGGAGGCCTTCGGGTTGTAAACCTCTTTTGTTAGGGAGCAAGGCACTTTGTGTTGAGTGTACCTTTCGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGTCCATCGCTTAACGGTGGATCCGCGCCGGGTACGGGCGGGCTTGAGTGCGGTAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCGAGTAGTC ++D +DDDDDDDCCCCFGGGGGGGGGGGGHHHHHHHCHHHHHHHGGGGGHGHHHHHHHHHGGGGGGGGGGGGGHGGHGGGHGGGHHHHGGHGGGHGHHHHHHHHHHHHHHHHHGGHHHGHHHHHGHHHFGHHHHHHHHHHHHHGGFGGHHHFHHGGGGGHHHGGGGGGGFFGGGGGGADFFFEFFFFFFFDFBAFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFDFFFFFF@DFFFFFFFFFFFFFFFFFFFFBDA9.;FFFFFFFFFFFDC@??D9?-?GGGGGGGGFGHEFGGHHGGFCFHHGHFFHHHHHGHHHHGCGGGCFHHGGC?GHHHHGHHHHEHHHHEGEEDFHHHHHGHGHHGF1GGGGHHHHHF3FHFG1HGGGGGEFFHHGGGGGHHHHHGGFGFHGGFEGGGGGGHGGGHHHHFGGGGGGGGGBBBBFBFBBBBB +@A +CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGCGGGATGGAGGCCTTCGGGTTGTAAACCGCTTTTGATCGGGAGCAAGCCCTTCGGGGTGAGTGTACCCTTCGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGCCCATCGCTTAACGGTGGGTCTGCGCCGGGTACGGGCGGGCTGGAGTGCGGTAGGGGAGACTGGAATTGCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCGCTGGGCCGTCACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCGGGTAGTA ++A +>AAAAAADADBBGGGGGGGGGGFGHHHHHGFHGHHHHHHGGGGEHFHHHHFHHHHGGEFFEFCGGGGGCGGGGGBCF?FHHHHGGHGGGHFHHHCDGGGHHFGHGGGGGGHHHEGEFHHH?DDDG.CGHBGFHHGGGG.;;.BFGFFGGAA?ABFB9FDAFEF/FFFAFFFFDAA.:FBBAB/AAE9ADFFFFDFBFFBFFFB;AF;FFF@EFFFBFFE>AEFFFFFE@B@@B-E@A?DFA-AACF/CAFFAB9------FFA9BAFBA-FEA9;@@A9-.C;9-A-@A@;AEF;FHHCCC@@<GEHGHHHGF111GF<>--//?G?1F/?</HGDG>GF1G>HGHGB/B//GG2F2GE??>111F/GCGHGEF0BEE>//0//E>///F12HFGGGGHGHHGAGCGGHGGEEEE0GGGHGGGGHHGGGGGBGGGF?ADDAFFFAA>11 +@B +CCTACGGGCGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAAGGACGACGTATTTCGGTATGTAAACTTCTATCAGCAAGGAAGATGATGACGGTACTTGACTAAGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGGCGGCCATGCAAGTCAGAAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTTGAAACTGTAAGGCTAGATTGCCGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTGAATGACGCTGAGGCTCGGAAGCGTGGGGAGCAAACAGGATTAGATACCCCAGTAGTA ++B +>>AAAA>DBBBBEGGGGGGGGGGGHHHHHHHHHHHHHHGGGGHHHGHHHHHHHHHGGGGGGGGGGGGGGHHHGGGGDHHHHHHGGHGHHHHHHHHHHHHHHHHFHHGHHHHHHHHHHHGGGHGHHHHHHHHHHHHHHFGGGGGGGGGFGGGGGGGGGGGGGBBBBFFFFFFFFFFFFFBBBFFFFFFFFFFFFFFFFFFFFFFBDBFFFFFFFFFFFFBFFFFBFBFFFFFFFFFFFFFFFFGFFFFFGGGFFE@A@CCGCHGHGFFG/GD00HHGGDBCBHDCFFFG><-?C<?GHGHHHGGGGGHHGGGD1CF0FGBC/CCAGGFGGEE/GFGBHGF2F1BHFHHHHGHBGEFFGGGFEHGGEECFD12BGFGGGHGHGDFHHGGGGHGHHGGGGGGHGGFGGGHGGGHHFHHFHFGGGGCFGGGGADA@BFFAA>11 +@chimeric_read +CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGCGGGATGGAGGCCTTCGGGTTGTAAACCGCTTTTGATCGGGAGCAAGCCCTTCGGGGTGAGTGTACCCTTCGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCCATGCAAGTCAGAAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTTGAAACTGTAAGGCTAGATTGCCGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTGAATGACGCTGAGGCTCGGAAGCGTGGGGAGCAAACAGGATTAGATACCCCAGTAGTA ++chimeric_read +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF |
| b |
| diff -r 000000000000 -r 2e150ed1b76e test-data/cd-hit-dup_out_chimera.chimeric_clusters.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cd-hit-dup_out_chimera.chimeric_clusters.tabular Wed Apr 29 12:06:47 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>Cluster 0 chimeric_parent1=0,chimeric_parent2=1 +0 440nt, >chimeric_read... * |
| b |
| diff -r 000000000000 -r 2e150ed1b76e test-data/cd-hit-dup_out_chimera.dup_clusters.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cd-hit-dup_out_chimera.dup_clusters.tabular Wed Apr 29 12:06:47 2015 -0400 |
| b |
| @@ -0,0 +1,10 @@ +>Cluster 0 +0 449nt, >A... * +1 449nt, >A2... at 1:449:1:449/+/100.00% +>Cluster 1 +0 440nt, >B... * +1 440nt, >B2... at 1:440:1:440/+/100.00% +>Cluster 2 +0 465nt, >C... * +>Cluster 3 +0 450nt, >D... * |
| b |
| diff -r 000000000000 -r 2e150ed1b76e test-data/cd-hit-dup_out_chimera.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cd-hit-dup_out_chimera.fastqsanger Wed Apr 29 12:06:47 2015 -0400 |
| b |
| @@ -0,0 +1,16 @@ +@A +CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGCGGGATGGAGGCCTTCGGGTTGTAAACCGCTTTTGATCGGGAGCAAGCCCTTCGGGGTGAGTGTACCCTTCGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGCCCATCGCTTAACGGTGGGTCTGCGCCGGGTACGGGCGGGCTGGAGTGCGGTAGGGGAGACTGGAATTGCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCGCTGGGCCGTCACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCGGGTAGTA ++A +>AAAAAADADBBGGGGGGGGGGFGHHHHHGFHGHHHHHHGGGGEHFHHHHFHHHHGGEFFEFCGGGGGCGGGGGBCF?FHHHHGGHGGGHFHHHCDGGGHHFGHGGGGGGHHHEGEFHHH?DDDG.CGHBGFHHGGGG.;;.BFGFFGGAA?ABFB9FDAFEF/FFFAFFFFDAA.:FBBAB/AAE9ADFFFFDFBFFBFFFB;AF;FFF@EFFFBFFE>AEFFFFFE@B@@B-E@A?DFA-AACF/CAFFAB9------FFA9BAFBA-FEA9;@@A9-.C;9-A-@A@;AEF;FHHCCC@@<GEHGHHHGF111GF<>--//?G?1F/?</HGDG>GF1G>HGHGB/B//GG2F2GE??>111F/GCGHGEF0BEE>//0//E>///F12HFGGGGHGHHGAGCGGHGGEEEE0GGGHGGGGHHGGGGGBGGGF?ADDAFFFAA>11 +@B +CCTACGGGCGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAAGGACGACGTATTTCGGTATGTAAACTTCTATCAGCAAGGAAGATGATGACGGTACTTGACTAAGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGGCGGCCATGCAAGTCAGAAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTTGAAACTGTAAGGCTAGATTGCCGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTGAATGACGCTGAGGCTCGGAAGCGTGGGGAGCAAACAGGATTAGATACCCCAGTAGTA ++B +>>AAAA>DBBBBEGGGGGGGGGGGHHHHHHHHHHHHHHGGGGHHHGHHHHHHHHHGGGGGGGGGGGGGGHHHGGGGDHHHHHHGGHGHHHHHHHHHHHHHHHHFHHGHHHHHHHHHHHGGGHGHHHHHHHHHHHHHHFGGGGGGGGGFGGGGGGGGGGGGGBBBBFFFFFFFFFFFFFBBBFFFFFFFFFFFFFFFFFFFFFFBDBFFFFFFFFFFFFBFFFFBFBFFFFFFFFFFFFFFFFGFFFFFGGGFFE@A@CCGCHGHGFFG/GD00HHGGDBCBHDCFFFG><-?C<?GHGHHHGGGGGHHGGGD1CF0FGBC/CCAGGFGGEE/GFGBHGF2F1BHFHHHHGHBGEFFGGGFEHGGEECFD12BGFGGGHGHGDFHHGGGGHGHHGGGGGGHGGFGGGHGGGHHFHHFHFGGGGCFGGGGADA@BFFAA>11 +@C +CCTACGGGCGGCTGCAGTGGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGAGTGATGACGGCCTTCGGGTTGTAAAGCTCTGTTAATCGGGACGAAAGGCCTTCTTGCGAATAGTGAGAAGGATTGACGGTACCGGAATAGAAAGCCACGGCTAGCTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGATAGGTCAGTCTGTCTTAAAAGTTCGGGGCTTAACCCCGTGATGGGATGGAAACTGCCAATCTAGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGACTTTCTGGACGAAAACTGACGCTGAGGCGCGAAAGCCAGGGGAGCGAACGGGATTAGATACCCGGGTAGTC ++C +ABBCCDCCCCCCGGGGGGGGGGGGHHHHHHGGGGGHHHHGGGGGHHHHHHGGGGGHHHGGGGGGGGGGHHHHHHHGGGGGHHHGGHGGGHHHHHHHHHHHHHHHGGGGGGGGGGHHHHHHHHHFG-DGGGGGGGGGGGGGGGFGGGGGGGGGGGFFFFFFFFFFFFFFFFFFBFFFFFFFHFFFFFFFFFFFFFFFHFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/B/FBFFGFBGFFGGGGFFAGGGGGGGFCGCDAGCGBHHHFFHHHHHGGGHFGD0HHHHHHGGGGGHHHHHHHHHEHHHHHFHHGHHHHHGGGGGHHHHHGGGGGHHHHHHHHGHHHHFHGHGFHHHGGGGHHGGGGGFGGHHHHGGGHGHHGHHGGGGGHHHGGGGGGGHHHHHHGGGGGHGGGHHHFFGGGGGGGGGBBBBFFFBBBA3 +@D +CCTACGGGTGGCTGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGGAGGCCTTCGGGTTGTAAACCTCTTTTGTTAGGGAGCAAGGCACTTTGTGTTGAGTGTACCTTTCGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGTCCATCGCTTAACGGTGGATCCGCGCCGGGTACGGGCGGGCTTGAGTGCGGTAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCGAGTAGTC ++D +DDDDDDDCCCCFGGGGGGGGGGGGHHHHHHHCHHHHHHHGGGGGHGHHHHHHHHHGGGGGGGGGGGGGHGGHGGGHGGGHHHHGGHGGGHGHHHHHHHHHHHHHHHHHGGHHHGHHHHHGHHHFGHHHHHHHHHHHHHGGFGGHHHFHHGGGGGHHHGGGGGGGFFGGGGGGADFFFEFFFFFFFDFBAFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFDFFFFFF@DFFFFFFFFFFFFFFFFFFFFBDA9.;FFFFFFFFFFFDC@??D9?-?GGGGGGGGFGHEFGGHHGGFCFHHGHFFHHHHHGHHHHGCGGGCFHHGGC?GHHHHGHHHHEHHHHEGEEDFHHHHHGHGHHGF1GGGGHHHHHF3FHFG1HGGGGGEFFHHGGGGGHHHHHGGFGFHGGFEGGGGGGHGGGHHHHFGGGGGGGGGBBBBFBFBBBBB |
| b |
| diff -r 000000000000 -r 2e150ed1b76e tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Apr 29 12:06:47 2015 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="cd-hit-auxtools" version="0.5-2012-03-07-fix-dan-gh-0.0.1"> + <repository changeset_revision="d0db9d974498" name="package_cd_hit_auxtools_0_5_2012_03_07_fix_dan" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |