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Commit message:
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit b9f62f2ab10f5ff1c56edb895323820df36bdd0e-dirty |
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modified:
tool_dependencies.xml |
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added:
coverage_sampler.xml test-data/csa_no_result test-data/csa_result test-data/ref.fa test-data/sampe.sam |
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removed:
gene_fraction.xml |
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| diff -r 72901052a829 -r fa1aae53a2f3 coverage_sampler.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/coverage_sampler.xml Tue Jun 28 23:31:46 2016 -0400 |
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| @@ -0,0 +1,80 @@ +<tool id="gene_fraction" name="Coverage Sampler" version="0.1.0"> + <description>A simple tool for calculating the amount of a gene that is covered by a sample of alignments</description> + <requirements> + <requirement type="package" version="0.1">csa</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + csa + -ref_fp $reference + -sam_fp $sam + -min $min + -max $max + -t $threshold + -skip $skip + -samples $samples + -out_fp $output + ]]></command> + <inputs> + <param type="data" name="reference" format="fasta" label="Reference sequence" /> + <param type="data" name="sam" format="sam" label="SAM file" /> + <param name="min" type="integer" label="Starting sample level" + value="1" min="1" max="100" help="(-min)" /> + <param name="max" type="integer" label="Ending sample level" + value="1" min="1" max="100" help="(-max)" /> + <param name="threshold" type="integer" label="Gene fraction threshold" + value="0" min="0" max="100" help="(-t)" /> + <param name="skip" type="integer" label="Amount of sample levels to skip" + value="1" min="1" max="100" help="(-skip)" /> + <param name="samples" type="integer" label="Iterations per sample level" + value="1" min="1" max="100" help="(-samples)" /> + </inputs> + <outputs> + <data name="output" format="tabular" /> + </outputs> + <tests> + <test> + <param name="reference" value="ref.fa"/> + <param name="sam" value="sampe.sam"/> + <param name="min" value="100"/> + <param name="max" value="100"/> + <param name="threshold" value="50"/> + <param name="skip" value="5"/> + <param name="samples" value="1"/> + <output name="output" file="csa_result" ftype="tabular"/> + </test> + <test> + <param name="reference" value="ref.fa"/> + <param name="sam" value="sampe.sam"/> + <param name="min" value="100"/> + <param name="max" value="100"/> + <param name="threshold" value="80"/> + <param name="skip" value="5"/> + <param name="samples" value="1"/> + <output name="output" file="csa_no_result" ftype="tabular"/> + </test> + </tests> + <help><![CDATA[ +A simple tool for calculating the amount of a gene that is covered by a sample of alignments. + +Program: Coverage Sampler + +Contact: Chris Dean <cdean11@rams.colostate.edu> + +Usage: csa [options] + +Options: + -ref_fp STR/FILE ref file path + -sam_fp STR/FILE sam file path + -min INT starting sample level + -max INT ending sample level + -skip INT amount of sample levels to skip + -t INT gene fraction threshold + -samples INT iterations per sample level + -out_fp STR/FILE output file path + ]]></help> + <citations> + </citations> +</tool> |
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| diff -r 72901052a829 -r fa1aae53a2f3 gene_fraction.xml --- a/gene_fraction.xml Wed Mar 23 17:54:53 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,63 +0,0 @@ -<tool id="gene_fraction" name="Coverage Sampler" version="0.1.0"> - <requirements> - <requirement type="package" version="0.1">csa</requirement> - </requirements> - <stdio> - <exit_code range="1:" /> - </stdio> - <description>Calculates the amount of a gene that is covered from a sample of reads</description> - <command><![CDATA[ - csa - -amr_fp $input1 - -sam_fp $input2 - -min $min - -max $max - -t $threshold - -skip $skip - -samples $samples - -out_fp $output1 - ]]></command> - <inputs> - <param type="data" name="input1" format="fasta" label="Reference sequence" /> - <param type="data" name="input2" format="sam" label="SAM file" /> - <param name="min" type="integer" label="Starting sample level" - value="1" min="1" max="100" help="(-min)" /> - <param name="max" type="integer" label="Ending sample level" - value="1" min="1" max="100" help="(-max)" /> - <param name="threshold" type="integer" label="Gene threshold" - value="0" min="0" max="100" help="(-t)" /> - <param name="skip" type="integer" label="Amount of levels to skip" - value="1" min="1" max="100" help="(-skip)" /> - <param name="samples" type="integer" label="Amount of samples per level" - value="1" min="1" max="100" help="(-samples)" /> - </inputs> - <outputs> - <data name="output1" format="tabular" /> - </outputs> - <tests> - <test> - <param name="input1" value="ref.fa"/> - <param name="input2" value="test.sam"/> - <output name="outfil1" file="out.txt"/> - </test> - </tests> - <help><![CDATA[ -This program takes iterative samples from a SAM file with the goal of identifying the amount of a gene that is covered by a sample of reads. - -Program: Coverage Sampler - -Contact: Chris Dean <cdean11@rams.colostate.edu> - -Usage: csa [options] - -Options: - -amr_fp amr database path - -sam_fp sam file path - -min starting level - -max ending level - -skip amount of levels to skip - -t gene fraction threshold - -samples amount of samples per level - -out_fp output file path - ]]></help> -</tool> |
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| diff -r 72901052a829 -r fa1aae53a2f3 test-data/csa_no_result --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/csa_no_result Tue Jun 28 23:31:46 2016 -0400 |
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| @@ -0,0 +1,1 @@ +Level Iteration Gene Id Gene Fraction Hits |
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| diff -r 72901052a829 -r fa1aae53a2f3 test-data/csa_result --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/csa_result Tue Jun 28 23:31:46 2016 -0400 |
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| @@ -0,0 +1,2 @@ +Level Iteration Gene Id Gene Fraction Hits +100 1 chr2:172936693-172938111 59.6615 20 |
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| diff -r 72901052a829 -r fa1aae53a2f3 test-data/ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref.fa Tue Jun 28 23:31:46 2016 -0400 |
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| @@ -0,0 +1,2 @@ +>chr2:172936693-172938111 +TTATGGCTTTAAAAATATTGTAACAGTGTCTGAATCAAACTTTAGTAAAATCTCTTTGGGTTATATCTGAGAAGCTTTTATTGAAGACTTTGAACAAAATTGTGTTTTTGACAGTTTTAAATTATAGGCTAACTAGCCTGGGAAAAAAGGATAGTGTCTCTCTGTTCTTTCATAGGAAATGTTGAATCAGACCCCTACTGGGAAAAGAAATTTAATGCATATCTCACTATCTTACTGTCCATGAATATAATAGAAATGAATTCAAAATGCAGTTTTATTTTTGCAAATGGGATGAGTCGATAGATGCACCTCATATTTTTGAACACCTAGGGTTCAACAAATTTACTGGTGGTGCTCTTGCATTTTAACAAAATTTATTCTTCAGTAGAAGGGGGCAGAGAACACTAGATTCTTATTCAAGCATTCTATCGAGCTCTGCATTCATGGCTGTGTCTAAAGGGCATGTCAGCCTTTGATTCTCTCTGAGAGGTAATTATCCTTTTCCTGTCACGGAACAACAAATGATAGCTAACTACAGAGGCACATTTGCAGTAGTCACATTCATCAACTGCAGAAAAAAAAATTCAATTTAATTGTGCAACACAGCTGCACATGGGCTTTTGAGCATTTCTGTTGTTCTCCCTGTCTCGCTATTCCTCCCTCCAGATCTATTTTTTAAACTTTTTTTCTGGTTATTTTTTCCCCTTTTTGTCTCTTCTTCCATTTTTACTCTCTGTACTTTCTTGTTAAAGTAATTTTCCTTTGTGGCTCTCATTCTTTTTCCCCCATTGAAGGCTATGAATGTAGAAAATTATCACAATTACTCATATAATTGAGCCTCTTTGTAGCAAGTGCAACTCCAGTAGCCTTTCTCCATCATGAAAATGGTTTCATTATAGGGTTTTTCATATTCTCTGACACCATCTACACAGAGGAACAGGCGTGCAGATGAGATGTGCTAGGAACAGGCTAGATCAGTAAGGTCACAGTAGGAATAATTAGCTCTGCTATGGAAAGAGCATCTAGGCCTTTTACTGCTACATAAATGTACTGTCCATGGCTTTTAGTCACAAAAAAAACTTACTAACAAATGGAGCTCCCGCCTACTACTTTGAAAAAAAGATTTGTATCAACACTACAATTTTCCATCATTAAGACTAATAACACAGAGCCTAGTATACATCAAGGGGAATAAAAAGAAAAATCTCACATTCAAGTGGCGGCTGGGTGCTGACCTTTGTTCCCTTTTTTTGTGTACGACTTAACTCTTTACAAAAAAGAGCCACACGCCACACCAACATGCAGGTGAACTCCAGCTAGTACTAGCAAAGCATAGCATTCAGTTGGAAAATTTGATAAATCTCCATGCAGGATAATGCATTTCATTACATATTCACTACATTAATTCTAGCTACATT |
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| diff -r 72901052a829 -r fa1aae53a2f3 test-data/sampe.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampe.sam Tue Jun 28 23:31:46 2016 -0400 |
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| @@ -0,0 +1,22 @@ +@SQ SN:chr2:172936693-172938111 LN:1418 +@PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa sampe ref.fa forward.sai reverse.sai lane1.fq lane2.fq +chr2:172936693-172938111_82_621_1:0:0_0:0:0_0 81 chr2:172936693-172938111 552 37 70M = 82 -540 GTAGTCACATTCATCAACTGCAGAAAAAAAAATTCAATTTAATTGTGCAACACAGCTGCACATGGGCTTT 2222222222222222222222222222222222222222222222222222222222222222222222 XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:70 +chr2:172936693-172938111_82_621_1:0:0_0:0:0_0 161 chr2:172936693-172938111 82 37 70M = 552 540 TGAAGACTTTGAACCAAATTGTGTTTTTGACAGTTTTAAATTATAGGCTAACTAGCCTGGGAAAAAAGGA 2222222222222222222222222222222222222222222222222222222222222222222222 XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:14A55 +chr2:172936693-172938111_127_617_0:0:0_2:0:0_1 99 chr2:172936693-172938111 127 60 70M = 548 491 GGCTAACTAGCCTGGGAAAAAAGGATAGTGTCTCTCTGTTCTTTCATAGGAAATGTTGAATCAGACCCCT 2222222222222222222222222222222222222222222222222222222222222222222222 XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:70 +chr2:172936693-172938111_127_617_0:0:0_2:0:0_1 147 chr2:172936693-172938111 548 60 70M = 127 -491 TGCAGTAGTCACATTCATCAACTGCAGAAAAAAAAATTCAAGTTAATGGTGCAACACAGCTGCACATGGG 2222222222222222222222222222222222222222222222222222222222222222222222 XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:41T5T22 +chr2:172936693-172938111_695_1174_2:0:0_0:0:0_2 83 chr2:172936693-172938111 1105 60 70M = 695 -480 TACTACTTTGAAAAAAAGATTTGTATCAACACTACAATTTTCCATCATTAAGACTAATAACACAGAGCCT 2222222222222222222222222222222222222222222222222222222222222222222222 XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:70 +chr2:172936693-172938111_695_1174_2:0:0_0:0:0_2 163 chr2:172936693-172938111 695 60 70M = 1105 480 ATTTTTTCCCCTTTTTGTCTGTTCTTCCATTTTTACTCTCTGTACTTTCTTGTAAAAGTAATTTTCCTTT 2222222222222222222222222222222222222222222222222222222222222222222222 XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:20C32T16 +chr2:172936693-172938111_675_1201_1:0:0_1:0:0_3 97 chr2:172936693-172938111 675 37 70M = 1132 527 TTTAAACTTTTTTTCTGGTTATTTTTTCCCCTTTTTGTCTCTTCTTCCATTTTTACTCTCTGTACTTTGT 2222222222222222222222222222222222222222222222222222222222222222222222 XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:68C1 +chr2:172936693-172938111_675_1201_1:0:0_1:0:0_3 145 chr2:172936693-172938111 1132 37 70M = 675 -527 AACACTACAATTTTCCATCTTTAAGACTAATAACACAGAGCCTAGTATACATCAAGGGGAATAAAAAGAA 2222222222222222222222222222222222222222222222222222222222222222222222 XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:19A50 +chr2:172936693-172938111_133_602_2:0:0_0:0:0_4 99 chr2:172936693-172938111 133 60 70M = 533 470 CTCGCGTGGGAAAAAAGGATAGTGTCTCTCTGTTCTTTCATAGGAAATGTTGAATCAGACCCCTACTGGG 2222222222222222222222222222222222222222222222222222222222222222222222 XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2A2C64 +chr2:172936693-172938111_133_602_2:0:0_0:0:0_4 147 chr2:172936693-172938111 533 60 70M = 133 -470 CTACAGAGGCACATTTGCAGTAGTCACATTCATCAACTGCAGAAAAAAAAATTCAATTTAATTGTGCAAC 2222222222222222222222222222222222222222222222222222222222222222222222 XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:70 +chr2:172936693-172938111_268_735_1:0:0_1:0:0_5 83 chr2:172936693-172938111 666 60 70M = 268 -468 CATCTATTTTTTAAACTTTTTTTCTGGTTATTTTTTCCCCTTTTTGTCTCTTCTTCCATTTTTACTCTCT 2222222222222222222222222222222222222222222222222222222222222222222222 XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0G69 +chr2:172936693-172938111_268_735_1:0:0_1:0:0_5 163 chr2:172936693-172938111 268 60 70M = 666 468 TGCAGATTTATTTTTGCAAATGGGATGAGTCGATAGATGCACCTCATATTTTTGAACACCTAGGGTTCAA 2222222222222222222222222222222222222222222222222222222222222222222222 XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:5T64 +chr2:172936693-172938111_380_811_2:0:0_1:0:0_6 99 chr2:172936693-172938111 380 60 70M = 742 432 CTTCAGTAGAAGGGGGCAGAGAACACTAGCTTCTTCTTCAAGCATTCTATCGAGCTCTGCATTCATGGCT 2222222222222222222222222222222222222222222222222222222222222222222222 XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:29A5A34 +chr2:172936693-172938111_380_811_2:0:0_1:0:0_6 147 chr2:172936693-172938111 742 60 70M = 380 -432 TCTTGTTAAAGTAATTTTCCTTTGTGGCTCTCATTCTTTTTCCCCCATTGAAGGCTAGGAATGTAGAAAA 2222222222222222222222222222222222222222222222222222222222222222222222 XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:57T12 +chr2:172936693-172938111_440_981_0:0:0_0:0:0_7 81 chr2:172936693-172938111 912 37 70M = 440 -542 TCTCTGACACCATCTACACAGAGGAACAGGCGTGCAGATGAGATGTGCTAGGAACAGGCTAGATCAGTAA 2222222222222222222222222222222222222222222222222222222222222222222222 XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:70 +chr2:172936693-172938111_440_981_0:0:0_0:0:0_7 161 chr2:172936693-172938111 440 37 70M = 912 542 ATTCATGGCTGTGTCTAAAGGGCATGTCAGCCTTTGATTCTCTCTGAGAGGTAATTATCCTTTTCCTGTC 2222222222222222222222222222222222222222222222222222222222222222222222 XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:70 +chr2:172936693-172938111_59_532_2:0:0_2:0:0_8 83 chr2:172936693-172938111 463 60 70M = 59 -474 ATGGCAGCCTTTGATTCTCTCTGAGAGGTAATTTTCCTTTTCCTGTCACGGAACAACAAATGATAGCTAA 2222222222222222222222222222222222222222222222222222222222222222222222 XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:3T29A36 +chr2:172936693-172938111_59_532_2:0:0_2:0:0_8 163 chr2:172936693-172938111 59 60 70M = 463 474 GGTTATATCTGAGAAGCTTTTATTGAAGACTTTGAACAAAATTGTGTTTTTGACAGTTTTCAATTATCGG 2222222222222222222222222222222222222222222222222222222222222222222222 XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:60A6A2 +chr2:172936693-172938111_642_1121_0:0:0_3:0:0_9 83 chr2:172936693-172938111 1052 60 70M = 642 -480 GGTCCATGGCTTTTAGTCACAAAAAAAACTTAATAACAAATGGAGCTCCCCCCTACTACTTTGAAAAAAA 2222222222222222222222222222222222222222222222222222222222222222222222 XT:A:U NM:i:3 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:3 XO:i:0 XG:i:0 MD:Z:0T31C17G19 +chr2:172936693-172938111_642_1121_0:0:0_3:0:0_9 163 chr2:172936693-172938111 642 60 70M = 1052 480 CCTGTCTCGCTATTCCTCCCTCCAGATCTATTTTTTAAACTTTTTTTCTGGTTATTTTTTCCCCTTTTTG 2222222222222222222222222222222222222222222222222222222222222222222222 XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:70 |
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| diff -r 72901052a829 -r fa1aae53a2f3 tool_dependencies.xml --- a/tool_dependencies.xml Wed Mar 23 17:54:53 2016 -0400 +++ b/tool_dependencies.xml Tue Jun 28 23:31:46 2016 -0400 |
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| @@ -3,7 +3,7 @@ <package name="csa" version="0.1"> <install version="1.0"> <actions> - <action type="shell_command">git clone --recursive https://github.com/ChrisD11/csa.git</action> + <action type="shell_command">git clone --recursive https://github.com/cdeanj/coverage_sampler.git</action> <action type="shell_command">make</action> <action type="move_file"> <source>csa</source> |