| Previous changeset 0:418b961e0576 (2017-08-10) Next changeset 2:d1015c2516b7 (2018-01-10) |
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Commit message:
planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36 |
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modified:
test-data/out_R1.fastq.gz test-data/out_R2.fastq.gz test-data/out_paired.log test-data/out_single.log umi-tools_extract.xml |
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added:
macros.xml test-data/group_in1.sam test-data/group_in2.bam test-data/group_in3.bam test-data/group_in4.bam test-data/group_in5.bam test-data/group_in6.bam test-data/group_out1.bam test-data/group_out2.bam test-data/group_out3.bam test-data/group_out3.tab test-data/group_out4.bam test-data/group_out4.tab test-data/group_out5.bam test-data/group_out6.bam |
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| diff -r 418b961e0576 -r 79436b3019e9 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Aug 29 17:37:07 2017 -0400 |
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| @@ -0,0 +1,23 @@ +<?xml version="1.0"?> +<macros> + <xml name="citations"> + <citations> + <citation type="doi">10.1101/gr.209601.116</citation> + <citation type="bibtex"> + @misc{githubUMI-tools, + title = {UMI-tools}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/CGATOxford/UMI-tools}, + } + </citation> + </citations> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">umi_tools</requirement> + <yield /> + </requirements> + </xml> + <token name="@VERSION@">0.5.0</token> +</macros> |
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| diff -r 418b961e0576 -r 79436b3019e9 test-data/group_in1.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/group_in1.sam Tue Aug 29 17:37:07 2017 -0400 |
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| b'@@ -0,0 +1,666 @@\n+@HD\tVN:1.0\tSO:coordinate\n+@PG\tID:Bowtie\tVN:1.1.2\tCL:"bowtie --wrapper basic-0 --threads 4 -v 2 -m 10 -a /ifs/mirror/genomes/bowtie/mm9 /dev/fd/63 --sam"\n+@SQ\tSN:chr10\tLN:129993255\n+@SQ\tSN:chr11\tLN:121843856\n+@SQ\tSN:chr12\tLN:121257530\n+@SQ\tSN:chr13\tLN:120284312\n+@SQ\tSN:chr14\tLN:125194864\n+@SQ\tSN:chr15\tLN:103494974\n+@SQ\tSN:chr16\tLN:98319150\n+@SQ\tSN:chr17\tLN:95272651\n+@SQ\tSN:chr18\tLN:90772031\n+@SQ\tSN:chr19\tLN:61342430\n+@SQ\tSN:chr1\tLN:197195432\n+@SQ\tSN:chr2\tLN:181748087\n+@SQ\tSN:chr3\tLN:159599783\n+@SQ\tSN:chr4\tLN:155630120\n+@SQ\tSN:chr5\tLN:152537259\n+@SQ\tSN:chr6\tLN:149517037\n+@SQ\tSN:chr7\tLN:152524553\n+@SQ\tSN:chr8\tLN:131738871\n+@SQ\tSN:chr9\tLN:124076172\n+@SQ\tSN:chrM\tLN:16299\n+@SQ\tSN:chrX\tLN:166650296\n+@SQ\tSN:chrY\tLN:15902555\n+SRR2057595.10000392_AAGTA\t16\tchr19\t31326011\t255\t57M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:23A33\tNM:i:1\tUG:i:512\tBX:Z:AAGTA\n+SRR2057595.10000468_GCTAT\t16\tchr19\t61240267\t255\t28M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:11C16\tNM:i:1\tUG:i:706\tBX:Z:GCTAT\n+SRR2057595.10000704_TGATG\t16\tchr19\t3544146\t255\t39M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:39\tNM:i:0\tUG:i:1\tBX:Z:TGATG\n+SRR2057595.10000838_TAGTA\t0\tchr19\t10274608\t255\t34M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:34\tNM:i:0\tUG:i:324\tBX:Z:TAGTA\n+SRR2057595.10001118_TCTCA\t16\tchr19\t4078298\t255\t50M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:43A6\tNM:i:1\tUG:i:36\tBX:Z:TCTCA\n+SRR2057595.10001329_CGGTC\t16\tchr19\t28083193\t255\t60M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:60\tNM:i:0\tUG:i:497\tBX:Z:CGGTC\n+SRR2057595.10001382_CTGCC\t16\tchr19\t3957282\t255\t22M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:17C1G2\tNM:i:2\tUG:i:9\tBX:Z:CTGCC\n+SRR2057595.10001382_CTGCC\t16\tchr19\t3970897\t255\t22M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:17C1G2\tNM:i:2\tUG:i:10\tBX:Z:CTGCC\n+SRR2057595.10002047_ATTAT\t16\tchr19\t7546213\t255\t27M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:27\tNM:i:0\tUG:i:278\tBX:Z:ATTAT\n+SRR2057595.10002219_ATCAG\t16\tchr19\t5796783\t255\t34M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:34\tNM:i:0\tUG:i:234\tBX:Z:ATCAG\n+SRR2057595.10002597_AATTA\t16\tchr19\t50733887\t255\t64M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:58C0C4\tNM:i:2\tUG:i:645\tBX:Z:AATTA\n+SRR2057595.10003084_GTCTA\t16\tchr19\t4078420\t255\t67M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:2T19A44\tNM:i:2\tUG:i:124\tBX:Z:GTCTA\n+SRR2057595.10003230_ACATT\t0\tchr19\t8799370\t255\t64M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:64\tNM:i:0\tUG:i:297\tBX:Z:ACATT\n+SRR2057595.10003317_CGGCC\t16\tchr19\t52641725\t255\t20M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:1C13A4\tNM:i:2\tUG:i:648\tBX:Z:CGGCC\n+SRR2057595.10003567_ATGTC\t0\tchr19\t37052811\t255\t64M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:11C52\tNM:i:1\tUG:i:542\tBX:Z:ATGTC\n+SRR2057595.10003576_AATCG\t16\tchr19\t4078303\t255\t67M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:38A21A6\tNM:i:2\tUG:i:88\tBX:Z:AATCG\n+SRR2057595.10003630_GTGTT\t16\tchr19\t4078298\t255\t52M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:42G0A8\tNM:i:2\tUG:i:45\tBX:Z:GTGTT\n+SRR2057595.10003869_TCTTG\t16\tchr19\t4078423\t255\t67M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:19A47\tNM:i:1\tUG:i:111\tBX:Z:TCTTG\n+SRR2057595.1000404_AACTT\t16\tchr19\t4078420\t255\t64M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:2T19A41\tNM:i:2\tUG:i:55\tBX:Z:AACTT\n+SRR2057595.10004161_TTCGC\t16\tchr19\t4078428\t255\t67M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:14A24T27\tNM:i:2\tUG:i:74\tBX:Z:TTCGC\n+SRR2057595.1000475_TCTGG\t0\tchr19\t13129234\t255\t28M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:22T5\tNM:i:1\tUG:i:383\tBX:Z:TCTGG\n+SRR2057595.10004845_GGATA\t0\tchr19\t24394180\t255\t29M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:11C15T1\tNM:i:2\tUG:i:481\tBX:Z:GGATA\n+SRR2057595.10005100_TTAAA\t16\tchr19\t4785463\t255\t21M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:21\tNM:i:0\tUG:i:196\tBX:Z:TTAAA\n+SRR2057595.10005761_CTAGA\t16\tchr19\t4078299\t255\t50M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:41G0A7\tNM:i:2\tUG:i:43\tBX:Z:CTAGA\n+SRR2057595.10005808_CAGTA\t16\tchr19\t7545872\t255\t24M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:24\tNM:i:0\tUG:i:276\tBX:Z:CAGTA\n+SRR2057595.10005955_GACAT\t16\tchr19\t4078302\t255\t67M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:39A21A5\tNM:i:2\tUG:i:82\tBX:Z:GACAT\n+SRR2057595.10006011_TCTCA\t16\tchr19\t4078298\t255\t50M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:43A6\tNM:i:1\tUG:i:36\tBX:Z:TCTCA\n+SRR2057595.10006546_GCTAC\t16\tchr19\t4078446\t255\t67M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:67\tNM:i:0\tUG:i:97\tBX:Z:GCTAC\n+SRR2057595.1000663_ACGCA\t16\tchr19\t51217013\t255\t67M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:3A46A16\tNM:i:2\tUG:i:647\tBX:Z:ACGCA\n+SRR2057595.10006870_GTCCA\t16\tchr19\t4078431\t255\t67M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:11A55\tNM:i:1\tUG:i:107\tBX:Z:GTCCA\n+SRR2057595.10006926_GGATA\t0\tchr19\t24394180\t255\t29M\t*\t0\t0\t*\t*\tXA:'..b'\tchr19\t55501486\t255\t31M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:8A22\tNM:i:1\tUG:i:659\tBX:Z:GATTG\n+SRR2057595.1013616_ATAGA\t0\tchr19\t38795805\t255\t62M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:46A15\tNM:i:1\tUG:i:553\tBX:Z:ATAGA\n+SRR2057595.10136267_TTCGC\t16\tchr19\t4078428\t255\t67M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:14A24T27\tNM:i:2\tUG:i:74\tBX:Z:TTCGC\n+SRR2057595.10136714_ATCCG\t16\tchr19\t37369602\t255\t35M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:35\tNM:i:0\tUG:i:544\tBX:Z:ATCCG\n+SRR2057595.10136765_GCTAT\t0\tchr19\t57701750\t255\t67M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:34T1T30\tNM:i:2\tUG:i:677\tBX:Z:GCTAT\n+SRR2057595.10137151_ATTCT\t0\tchr19\t3576314\t255\t23M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:16T5T0\tNM:i:2\tUG:i:5\tBX:Z:ATTCT\n+SRR2057595.10137262_ACAAA\t16\tchr19\t4078298\t255\t49M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:43A5\tNM:i:1\tUG:i:27\tBX:Z:ACAAA\n+SRR2057595.10137317_GATTG\t0\tchr19\t8799830\t255\t67M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:67\tNM:i:0\tUG:i:314\tBX:Z:GATTG\n+SRR2057595.10137603_GCTAT\t16\tchr19\t61240267\t255\t28M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:11C16\tNM:i:1\tUG:i:706\tBX:Z:GCTAT\n+SRR2057595.10137788_TAGTA\t0\tchr19\t10274608\t255\t34M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:34\tNM:i:0\tUG:i:324\tBX:Z:TAGTA\n+SRR2057595.1013793_GCGCA\t0\tchr19\t8798523\t255\t30M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:30\tNM:i:0\tUG:i:295\tBX:Z:GCGCA\n+SRR2057595.10138029_GTTGT\t16\tchr19\t12564367\t255\t21M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:0A12A7\tNM:i:2\tUG:i:380\tBX:Z:GTTGT\n+SRR2057595.10138656_CTAGC\t16\tchr19\t4078298\t255\t62M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:43A18\tNM:i:1\tUG:i:63\tBX:Z:CTAGC\n+SRR2057595.10138697_GCCGT\t0\tchr19\t30861987\t255\t20M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:3C2T13\tNM:i:2\tUG:i:511\tBX:Z:GCCGT\n+SRR2057595.10138764_GATGG\t0\tchr19\t44417644\t255\t23M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:15T4C2\tNM:i:2\tUG:i:601\tBX:Z:GATGG\n+SRR2057595.10138897_TGATT\t16\tchr19\t4078299\t255\t50M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:41G0A7\tNM:i:2\tUG:i:41\tBX:Z:TGATT\n+SRR2057595.10139239_GAGTG\t0\tchr19\t8798502\t255\t51M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:51\tNM:i:0\tUG:i:289\tBX:Z:GAGTG\n+SRR2057595.10139499_AGTCT\t0\tchr19\t13129558\t255\t37M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:21A15\tNM:i:1\tUG:i:398\tBX:Z:AGTCT\n+SRR2057595.10139596_GCTAC\t16\tchr19\t4078446\t255\t67M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:67\tNM:i:0\tUG:i:97\tBX:Z:GCTAC\n+SRR2057595.10139652_GGATG\t0\tchr19\t13129322\t255\t27M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:27\tNM:i:0\tUG:i:402\tBX:Z:GGATG\n+SRR2057595.10139674_ATGAA\t16\tchr19\t4078298\t255\t37M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:37\tNM:i:0\tUG:i:175\tBX:Z:ATAAA\n+SRR2057595.10139952_TAGTA\t16\tchr19\t61240268\t255\t27M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:10C16\tNM:i:1\tUG:i:702\tBX:Z:TAGTA\n+SRR2057595.10140058_ATATA\t0\tchr19\t13129330\t255\t22M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:0T21\tNM:i:1\tUG:i:422\tBX:Z:ATATA\n+SRR2057595.10141122_GTCCC\t0\tchr19\t12347657\t255\t32M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:32\tNM:i:0\tUG:i:372\tBX:Z:GTCCC\n+SRR2057595.10141122_GTCCC\t0\tchr19\t12348043\t255\t32M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:32\tNM:i:0\tUG:i:374\tBX:Z:GTCCC\n+SRR2057595.10141122_GTCCC\t16\tchr19\t15035071\t255\t32M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:29T2\tNM:i:1\tUG:i:428\tBX:Z:GTCCC\n+SRR2057595.10141295_TAGTA\t0\tchr19\t10274608\t255\t34M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:34\tNM:i:0\tUG:i:324\tBX:Z:TAGTA\n+SRR2057595.10142441_GTCTA\t16\tchr19\t4078420\t255\t67M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:2T19A44\tNM:i:2\tUG:i:124\tBX:Z:GTCTA\n+SRR2057595.10142482_GCCGA\t16\tchr19\t7389994\t255\t48M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:47C0\tNM:i:1\tUG:i:274\tBX:Z:GCCGA\n+SRR2057595.10143102_AAGTA\t16\tchr19\t31326011\t255\t57M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:23A33\tNM:i:1\tUG:i:512\tBX:Z:AAGTA\n+SRR2057595.10143387_GCATA\t16\tchr19\t4078298\t255\t57M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:42G0A13\tNM:i:2\tUG:i:53\tBX:Z:GCATA\n+SRR2057595.10143631_ATTTT\t0\tchr19\t45095257\t255\t57M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:57\tNM:i:0\tUG:i:606\tBX:Z:ATTTT\n+SRR2057595.10143687_CGCTT\t0\tchr19\t13129322\t255\t26M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:26\tNM:i:0\tUG:i:406\tBX:Z:CGCTT\n+SRR2057595.10143772_TGATT\t16\tchr19\t4078299\t255\t50M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:41G0A7\tNM:i:2\tUG:i:41\tBX:Z:TGATT\n+SRR2057595.10143909_CAGAC\t0\tchr19\t5493782\t255\t41M\t*\t0\t0\t*\t*\tXA:i:0\tMD:Z:41\tNM:i:0\tUG:i:218\tBX:Z:CAGAC\n+SRR2057595.10143972_CTTAC\t16\tchr19\t4078298\t255\t54M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:42G0A10\tNM:i:2\tUG:i:49\tBX:Z:CTTAC\n+SRR2057595.10144216_CATAA\t0\tchr19\t13129322\t255\t35M\t*\t0\t0\t*\t*\tXA:i:1\tMD:Z:33C1\tNM:i:1\tUG:i:401\tBX:Z:CATAA\n+SRR2057595.10144367_ATGAT\t16\tchr19\t61240306\t255\t36M\t*\t0\t0\t*\t*\tXA:i:2\tMD:Z:16A4T14\tNM:i:2\tUG:i:716\tBX:Z:ATGAT\n' 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| diff -r 418b961e0576 -r 79436b3019e9 test-data/group_out3.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/group_out3.tab Tue Aug 29 17:37:07 2017 -0400 |
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| b'@@ -0,0 +1,498 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GG\tchrM\t14783\tNA\tGG\t1\tGG\t1\t437\n+chrM_14314_14802_5:0:0_3:0:0_191/1_GG\tchrM\t14802\tNA\tGG\t1\tGG\t1\t438\n+chrM_14817_15261_5:0:0_4:0:0_65/1_AT\tchrM\t14816\tNA\tAT\t1\tAT\t1\t439\n+chrM_14863_15320_2:0:0_4:0:0_d8/1_AA\tchrM\t14862\tNA\tAA\t1\tAA\t1\t440\n+chrM_14869_15387_2:0:0_7:0:0_1f/1_AC\tchrM\t14868\tNA\tAC\t1\tAC\t1\t441\n+chrM_14888_15340_3:0:0_3:0:0_112/1_GG\tchrM\t14887\tNA\tGG\t1\tGG\t1\t442\n+chrM_14368_14894_6:0:0_5:0:0_40/1_TC\tchrM\t14894\tNA\tTC\t1\tTC\t1\t443\n+chrM_14410_14941_6:0:0_3:0:0_e5/1_TA\tchrM\t14941\tNA\tTA\t1\tTA\t1\t444\n+chrM_14962_15543_5:0:0_8:0:0_46/1_CA\tchrM\t14961\tNA\tCA\t1\tCA\t1\t445\n+chrM_14456_14987_3:0:0_5:0:0_ab/1_GT\tchrM\t14987\tNA\tGT\t1\tGT\t1\t446\n+chrM_15070_15569_5:0:0_5:0:0_cf/1_CA\tchrM\t15069\tNA\tCA\t1\tCA\t1\t447\n+chrM_15140_15686_2:0:0_5:0:0_185/1_CC\tchrM\t15139\tNA\tCC\t1\tCC\t1\t448\n+chrM_15142_15661_7:0:0_3:0:0_11e/1_CT\tchrM\t15141\tNA\tCT\t1\tCT\t1\t449\n+chrM_15192_15694_5:0:0_2:0:0_f7/1_CA\tchrM\t15191\tNA\tCA\t1\tCA\t1\t450\n+chrM_15211_15685_5:0:0_2:0:0_1d7/1_AC\tchrM\t15210\tNA\tAC\t1\tAC\t1\t451\n+chrM_15225_15786_3:0:0_6:0:0_17e/1_TT\tchrM\t15224\tNA\tTT\t1\tTT\t1\t452\n+chrM_15258_15810_4:0:0_6:0:0_5f/1_TT\tchrM\t15257\tNA\tTT\t1\tTT\t1\t453\n+chrM_14817_15317_5:0:0_2:0:0_59/1_GC\tchrM\t15317\tNA\tGC\t1\tGC\t1\t454\n+chrM_15324_15836_4:0:0_3:0:0_94/1_AC\tchrM\t15323\tNA\tAC\t1\tAC\t1\t455\n+chrM_15365_15880_4:1:0_3:0:0_80/1_CA\tchrM\t15364\tNA\tCA\t1\tCA\t1\t456\n+chrM_15408_15863_2:1:0_3:0:0_1e6/1_AG\tchrM\t15407\tNA\tAG\t1\tAG\t1\t457\n+chrM_15439_15924_0:0:0_4:0:0_172/1_TG\tchrM\t15438\tNA\tTG\t1\tTG\t1\t458\n+chrM_14931_15457_2:0:0_4:1:0_1a1/1_AA\tchrM\t15457\tNA\tAA\t1\tAA\t1\t459\n+chrM_15547_16054_5:0:0_1:0:0_af/1_GA\tchrM\t15546\tNA\tGA\t1\tGA\t1\t460\n+chrM_15134_15560_3:0:0_4:0:0_1c4/1_GG\tchrM\t15560\tNA\tGG\t1\tGG\t1\t461\n+chrM_15575_16118_5:0:0_4:0:0_1aa/1_GC\tchrM\t15574\tNA\tGC\t1\tGC\t1\t462\n+chrM_15052_15629_7:0:0_9:0:0_15f/1_GA\tchrM\t15629\tNA\tGA\t1\tGA\t1\t463\n+chrM_15698_16224_5:0:0_6:0:0_138/1_AC\tchrM\t15697\tNA\tAC\t1\tAC\t1\t464\n+chrM_15247_15721_2:1:0_6:0:0_17/1_TC\tchrM\t15721\tNA\tTC\t1\tTC\t1\t465\n+chrM_15218_15763_2:0:0_2:0:0_171/1_AG\tchrM\t15763\tNA\tAG\t1\tAG\t1\t466\n+chrM_15860_16419_5:0:0_8:0:0_53/1_TA\tchrM\t15859\tNA\tTA\t1\tTA\t1\t467\n+chrM_15864_16329_3:0:0_3:0:0_18b/1_CG\tchrM\t15863\tNA\tCG\t1\tCG\t1\t468\n+chrM_15507_15962_3:0:0_0:0:0_5b/1_GT\tchrM\t15962\tNA\tGT\t1\tGT\t1\t469\n+chrM_15430_15985_5:0:0_3:0:0_2c/1_AT\tchrM\t15985\tNA\tAT\t1\tAT\t1\t470\n+chrM_15706_16238_6:0:0_7:0:0_7b/1_AG\tchrM\t16238\tNA\tAG\t1\tAG\t1\t471\n+chrM_16252_16701_2:1:0_5:0:0_147/1_TA\tchrM\t16251\tNA\tTA\t1\tTA\t1\t472\n+chrM_15753_16280_5:0:0_6:0:0_180/1_TG\tchrM\t16280\tNA\tTG\t1\tTG\t1\t473\n+chrM_15777_16347_2:0:0_6:0:0_16/1_AT\tchrM\t16347\tNA\tAT\t1\tAT\t1\t474\n+chrM_16366_16911_6:1:0_6:1:1_168/1_CC\tchrM\t16365\tNA\tCC\t1\tCC\t1\t475\n+chrM_16370_16833_6:1:0_6:0:1_1bb/1_AC\tchrM\t16369\tNA\tAC\t1\tAC\t1\t476\n+chrM_16402_16876_2:0:0_1:0:1_98/1_CA\tchrM\t16401\tNA\tCA\t1\tCA\t1\t477\n+chrM_16426_16953_3:0:0_2:2:0_60/1_AA\tchrM\t16425\tNA\tAA\t1\tAA\t1\t478\n+chrM_15986_16442_3:0:0_7:0:0_15d/1_TG\tchrM\t16442\tNA\tTG\t1\tTG\t1\t479\n+chrM_16030_16460_6:0:0_4:1:0_20/1_AT\tchrM\t16460\tNA\tAT\t1\tAT\t1\t480\n+chrM_15909_16463_3:0:0_7:1:0_106/1_GT\tchrM\t16463\tNA\tGT\t1\tGT\t1\t481\n+chrM_15984_16500_4:0:0_1:0:0_6b/1_GT\tchrM\t16500\tNA\tGT\t1\tGT\t1\t482\n+chrM_16070_16513_3:0:0_7:1:0_1e7/1_TA\tchrM\t16513\tNA\tTA\t1\tTA\t1\t483\n+chrM_16064_16572_4:0:0_6:1:0_f1/1_TG\tchrM\t16572\tNA\tTG\t1\tTG\t1\t484\n+chrM_16245_16740_4:1:0_2:0:1_127/1_TA\tchrM\t16742\tNA\tTA\t1\tTA\t1\t485\n+chrM_16315_16834_5:0:0_3:0:1_18/1_TT\tchrM\t16834\tNA\tTT\t1\tTT\t1\t486\n+chrM_16229_16843_2:1:0_2:0:1_c4/1_GC\tchrM\t16843\tNA\tGC\t1\tGC\t1\t487\n+chrM_16420_16905_5:0:0_2:0:1_159/1_GT\tchrM\t16905\tNA\tGT\t2\tGT\t2\t488\n+chrM_16420_16905_5:0:0_2:0:1_159/1_GT\tchrM\t16905\tNA\tGT\t2\tGT\t2\t488\n+chrM_16419_16923_3:0:0_3:0:1_183/1_CG\tchrM\t16923\tNA\tCG\t1\tCG\t1\t489\n+chrM_16585_16993_5:0:1_5:1:0_1b9/1_GA\tchrM\t16993\tNA\tGA\t1\tGA\t1\t490\n' 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| diff -r 418b961e0576 -r 79436b3019e9 test-data/out_paired.log --- a/test-data/out_paired.log Thu Aug 10 06:37:09 2017 -0400 +++ b/test-data/out_paired.log Tue Aug 29 17:37:07 2017 -0400 |
| b |
| @@ -1,116 +1,36 @@ -# output generated by extract --bc-pattern=NNNXXX --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz --log=/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_863.dat -# job started at Tue Aug 8 15:14:12 2017 on packer-test -- cba9bf6d-f8cd-49c4-8184-3f4a090cbc3e -# pid: 32709, system: Linux 4.4.0-83-generic #106-Ubuntu SMP Mon Jun 26 17:54:43 UTC 2017 x86_64 +# output generated by extract --bc-pattern=NNNXXX --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz --log=/tmp/tmpREDhtd/files/003/dataset_3773.dat +# job started at Tue Aug 29 14:20:44 2017 on gaius -- 5913ff4c-b1d1-4f65-abec-66ca6684bdbd +# pid: 21437, system: Linux 4.10.0-33-generic #37-Ubuntu SMP Fri Aug 11 10:55:28 UTC 2017 x86_64 +# blacklist : None +# compresslevel : 6 +# error_correct_cell : False +# extract_method : string +# filter_cell_barcode : None +# filter_cell_barcodes : False # log2stderr : False # loglevel : 1 # pattern : NNNXXX # pattern2 : None -# prime3 : False +# prime3 : None # quality_encoding : None +# quality_filter_mask : None # quality_filter_threshold : None # random_seed : None # read2_in : input_read2.gz # read2_out : out2.gz +# read2_stdout : False +# reads_subset : None +# reconcile : False # short_help : None -# split : False -# stats : True # stderr : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='UTF-8'> # stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'> -# stdlog : <_io.TextIOWrapper name='/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_863.dat' mode='a' encoding='UTF-8'> +# stdlog : <_io.TextIOWrapper name='/tmp/tmpREDhtd/files/003/dataset_3773.dat' mode='a' encoding='UTF-8'> # stdout : <_io.TextIOWrapper name='out1.gz' encoding='ascii'> # timeit_file : None # timeit_header : None # timeit_name : all -Barcode UMI Sample Count -AAAAGT AAA AGT 1 -TTTTTT TTT TTT 1 -TTGGTT TTG GTT 1 -AAGTTT AAG TTT 1 -ATATAA ATA TAA 1 -GTTTTT GTT TTT 4 -GTTTTA GTT TTA 1 -TATAGA TAT AGA 1 -AAGTAT AAG TAT 1 -TTATTT TTA TTT 1 -AGATGA AGA TGA 1 -TTTTAG TTT TAG 2 -GTGTTT GTG TTT 1 -GTATGT GTA TGT 1 -AGTGTT AGT GTT 1 -AGAAAT AGA AAT 1 -TATAAA TAT AAA 1 -TGTATC TGT ATC 1 -TAAAAT TAA AAT 1 -ATTATT ATT ATT 1 -ATTTAG ATT TAG 1 -TATATT TAT ATT 1 -ATTTGG ATT TGG 1 -AAAATA AAA ATA 1 -AAGTTA AAG TTA 1 -GTTGTA GTT GTA 1 -TTTGAA TTT GAA 1 -ATTTGA ATT TGA 1 -TTTATA TTT ATA 2 -ATACGT ATA CGT 1 -GGTTAG GGT TAG 1 -GGTGTT GGT GTT 1 -TGGTTG TGG TTG 1 -AGTTAT AGT TAT 1 -GAGTAG GAG TAG 1 -TGTGTT TGT GTT 1 -TGAATT TGA ATT 1 -TTTAGG TTT AGG 2 -TAGATG TAG ATG 1 -TTGGAT TTG GAT 1 -TTGGAC TTG GAC 1 -TGTATG TGT ATG 1 -AGAGTG AGA GTG 1 -AGAATA AGA ATA 1 -TTGTTT TTG TTT 1 -AATATA AAT ATA 1 -TTATTA TTA TTA 1 -TTAAAG TTA AAG 2 -AGGAGT AGG AGT 1 -ATAAGT ATA AGT 1 -TTGTGG TTG TGG 1 -GTATTA GTA TTA 1 -AGTGGA AGT GGA 1 -TTTGGG TTT GGG 1 -TAAGAG TAA GAG 1 -TTGGGA TTG GGA 1 -TATAGG TAT AGG 1 -TTTTTG TTT TTG 1 -AAGAGG AAG AGG 1 -GAGAGA GAG AGA 1 -TTGGTG TTG GTG 1 -TAGAGG TAG AGG 1 -ATTTTG ATT TTG 1 -TGGATG TGG ATG 1 -ATTTTT ATT TTT 1 -TTATAT TTA TAT 1 -TGTTTG TGT TTG 1 -GTTGGT GTT GGT 1 -TCTTTA TCT TTA 1 -ATTGTT ATT GTT 2 -ATAAGA ATA AGA 1 -TATCGA TAT CGA 1 -TTTGTT TTT GTT 1 -GTGTAT GTG TAT 1 -AGTGAA AGT GAA 1 -GTTGTG GTT GTG 1 -TAGTGA TAG TGA 1 -TATTGA TAT TGA 1 -TTAATG TTA ATG 1 -TTTAAA TTT AAA 2 -AGAAAG AGA AAG 1 -TTTTGT TTT TGT 1 -TTATAG TTA TAG 1 -AGGTGT AGG TGT 1 -TTAGTT TTA GTT 1 -TTTAAT TTT AAT 1 -AGGATG AGG ATG 1 -ATATAT ATA TAT 1 -AGAGTT AGA GTT 1 -GAGAAA GAG AAA 1 -ATATGA ATA TGA 1 -# job finished in 0 seconds at Tue Aug 8 15:14:12 2017 -- 0.41 0.02 0.00 0.00 -- cba9bf6d-f8cd-49c4-8184-3f4a090cbc3e +# whitelist : None +2017-08-29 14:20:44,451 INFO Starting barcode extraction +2017-08-29 14:20:44,461 INFO Input Reads: 100 +2017-08-29 14:20:44,461 INFO Reads output: 100 +# job finished in 0 seconds at Tue Aug 29 14:20:44 2017 -- 0.73 0.05 0.00 0.00 -- 5913ff4c-b1d1-4f65-abec-66ca6684bdbd |
| b |
| diff -r 418b961e0576 -r 79436b3019e9 test-data/out_single.log --- a/test-data/out_single.log Thu Aug 10 06:37:09 2017 -0400 +++ b/test-data/out_single.log Tue Aug 29 17:37:07 2017 -0400 |
| b |
| @@ -1,92 +1,37 @@ -# output generated by extract --bc-pattern=XXXNNN --stdin=/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_867.dat --stdout /home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_886.dat --3prime --quality-filter-threshold 10 --quality-encoding phred33 --log=/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_887.dat -# job started at Wed Aug 9 09:51:05 2017 on packer-test -- e5896848-87b1-4bf4-a96c-b7a4a83a0b8b -# pid: 7652, system: Linux 4.4.0-83-generic #106-Ubuntu SMP Mon Jun 26 17:54:43 UTC 2017 x86_64 +# output generated by extract --bc-pattern=XXXNNN --stdin=/tmp/tmpREDhtd/files/003/dataset_3766.dat --stdout /tmp/tmpREDhtd/files/003/dataset_3767.dat --3prime --quality-filter-threshold 10 --quality-encoding phred33 --log=/tmp/tmpREDhtd/files/003/dataset_3768.dat +# job started at Tue Aug 29 14:20:26 2017 on gaius -- 1cfd46e7-5d74-4c25-8cdd-89cf8f41a393 +# pid: 21338, system: Linux 4.10.0-33-generic #37-Ubuntu SMP Fri Aug 11 10:55:28 UTC 2017 x86_64 +# blacklist : None +# compresslevel : 6 +# error_correct_cell : False +# extract_method : string +# filter_cell_barcode : None +# filter_cell_barcodes : False # log2stderr : False # loglevel : 1 # pattern : XXXNNN # pattern2 : None # prime3 : True # quality_encoding : phred33 +# quality_filter_mask : None # quality_filter_threshold : 10 # random_seed : None # read2_in : None -# read2_out : None +# read2_out : False +# read2_stdout : False +# reads_subset : None +# reconcile : False # short_help : None -# split : False -# stats : True # stderr : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='UTF-8'> -# stdin : <_io.TextIOWrapper name='/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_867.dat' mode='r' encoding='UTF-8'> -# stdlog : <_io.TextIOWrapper name='/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_887.dat' mode='a' encoding='UTF-8'> -# stdout : <_io.TextIOWrapper name='/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_886.dat' mode='w' encoding='UTF-8'> +# stdin : <_io.TextIOWrapper name='/tmp/tmpREDhtd/files/003/dataset_3766.dat' mode='r' encoding='UTF-8'> +# stdlog : <_io.TextIOWrapper name='/tmp/tmpREDhtd/files/003/dataset_3768.dat' mode='a' encoding='UTF-8'> +# stdout : <_io.TextIOWrapper name='/tmp/tmpREDhtd/files/003/dataset_3767.dat' mode='w' encoding='UTF-8'> # timeit_file : None # timeit_header : None # timeit_name : all -Barcode UMI Sample Count -AAGTTA TTA AAG 1 -GGATTT TTT GGA 1 -GGATAG TAG GGA 1 -TTTTTT TTT TTT 4 -GAGAGG AGG GAG 1 -TTAGTT GTT TTA 1 -TGTAGA AGA TGT 1 -AGAGAT GAT AGA 1 -GAATAA TAA GAA 1 -TTGAGT AGT TTG 1 -TTTATT ATT TTT 1 -GTAAGG AGG GTA 1 -GAAGAG GAG GAA 1 -TGTTTG TTG TGT 1 -ATAATG ATG ATA 1 -TTAGAT GAT TTA 1 -GTCTGA TGA GTC 1 -ATCATC ATC ATC 1 -GTCACC ACC GTC 1 -AACTCC TCC AAC 1 -TTATTA TTA TTA 1 -TGTTGT TGT TGT 2 -GTTTAT TAT GTT 1 -ATGAGT AGT ATG 1 -ATAATT ATT ATA 1 -TTGGTT GTT TTG 1 -GTTTTG TTG GTT 1 -CACGTC GTC CAC 1 -TTGTGT TGT TTG 1 -TGAATT ATT TGA 1 -GGATGT TGT GGA 1 -AGTCAC CAC AGT 1 -GTTTTT TTT GTT 1 -TATAGT AGT TAT 1 -TTTTAT TAT TTT 1 -TAAAAA AAA TAA 1 -ATAGGT GGT ATA 1 -ATTTTA TTA ATT 1 -TGTATA ATA TGT 1 -TGTTTT TTT TGT 2 -AGATTT TTT AGA 1 -TAGAAT AAT TAG 1 -GAAGGA GGA GAA 1 -GTTTGA TGA GTT 1 -TTTTGT TGT TTT 1 -ATTTTT TTT ATT 1 -TGTTAT TAT TGT 1 -CAGGAT GAT CAG 1 -GTATTT TTT GTA 1 -TGGGTA GTA TGG 1 -AAAGTT GTT AAA 1 -GGTGTG GTG GGT 1 -AAGATC ATC AAG 1 -TAGGTT GTT TAG 1 -GAGTTA TTA GAG 1 -TTATTT TTT TTA 1 -GTTGTT GTT GTT 1 -AGGTTT TTT AGG 1 -TAAAGT AGT TAA 1 -AGTTTT TTT AGT 1 -TTTGAT GAT TTT 1 -ATAAAT AAT ATA 1 -GTTATT ATT GTT 1 -TTTTTA TTA TTT 1 -AAGTGT TGT AAG 1 -ATATAG TAG ATA 1 -TATAGA AGA TAT 1 -# job finished in 0 seconds at Wed Aug 9 09:51:05 2017 -- 0.36 0.02 0.00 0.00 -- e5896848-87b1-4bf4-a96c-b7a4a83a0b8b +# whitelist : None +2017-08-29 14:20:26,493 INFO Starting barcode extraction +2017-08-29 14:20:26,495 INFO Input Reads: 100 +2017-08-29 14:20:26,495 INFO Reads output: 72 +2017-08-29 14:20:26,495 INFO filtered: umi quality: 28 +# job finished in 0 seconds at Tue Aug 29 14:20:26 2017 -- 0.75 0.02 0.00 0.00 -- 1cfd46e7-5d74-4c25-8cdd-89cf8f41a393 |
| b |
| diff -r 418b961e0576 -r 79436b3019e9 umi-tools_extract.xml --- a/umi-tools_extract.xml Thu Aug 10 06:37:09 2017 -0400 +++ b/umi-tools_extract.xml Tue Aug 29 17:37:07 2017 -0400 |
| [ |
| @@ -1,8 +1,9 @@ -<tool id="umi_tools_extract" name="UMI-tools extract" version="0.4.4.0"> +<tool id="umi_tools_extract" name="UMI-tools extract" version="@VERSION@.0"> <description>Extract UMI from fastq files</description> - <requirements> - <requirement type="package" version="0.4.4">umi_tools</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ #set $gz = False #if $input_type.type == 'single': @@ -150,16 +151,16 @@ <param name="quality_filter_threshold" value="10" /> <param name="quality_encoding" value="phred33" /> <output name="out" file="out_SE.fastq" /> - <output name="out_log" file="out_single.log" lines_diff="15"/> + <output name="out_log" file="out_single.log" lines_diff="22"/> </test> <test> <param name="type" value="paired" /> <param name="input_read1" value="t_R1.fastq.gz" ftype="fastq.gz" /> <param name="input_read2" value="t_R2.fastq.gz" ftype="fastq.gz" /> <param name="bc_pattern" value="NNNXXX" /> - <output name="out1" file="out_R1.fastq.gz" decompress="true" /> - <output name="out2" file="out_R2.fastq.gz" decompress="true" /> - <output name="out_log" file="out_paired.log" lines_diff="10"/> + <output name="out1" file="out_R1.fastq.gz" decompress="true" lines_diff="2" /> + <output name="out2" file="out_R2.fastq.gz" decompress="true" lines_diff="2" /> + <output name="out_log" file="out_paired.log" lines_diff="16"/> </test> </tests> <help><![CDATA[ @@ -241,15 +242,5 @@ and end two to FASTQOUT. ]]></help> - <citations> - <citation type="doi">10.1101/gr.209601.116</citation> - <citation type="bibtex"> - @misc{githubUMI-tools, - title = {UMI-tools}, - publisher = {GitHub}, - journal = {GitHub repository}, - url = {https://github.com/CGATOxford/UMI-tools}, - } - </citation> - </citations> + <expand macro="citations" /> </tool> |