| Previous changeset 7:8250ea3a1501 (2021-02-10) Next changeset 9:24013bf85a6f (2021-10-23) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" |
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modified:
macros.xml test-data/dedup_out1.bam test-data/dedup_out2.bam test-data/dedup_out3.bam test-data/dedup_out4.bam test-data/dedup_out5.bam test-data/dedup_out6.bam test-data/group_out4.bam test-data/group_out4.tab test-data/out_wl_paired.log umi-tools_counts.xml |
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added:
test-data/chr19_gene_tags.sam test-data/group_in2.sam |
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| diff -r 8250ea3a1501 -r e654095ab143 macros.xml --- a/macros.xml Wed Feb 10 19:29:55 2021 +0000 +++ b/macros.xml Mon Sep 13 14:49:44 2021 +0000 |
| [ |
| b'@@ -1,5 +1,43 @@\n <?xml version="1.0"?>\n <macros>\n+\n+ <!-- macros applying to all umi_tools -->\n+\n+ <token name="@TOOL_VERSION@">1.1.2</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@PROFILE@">21.01</token>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">umi_tools</requirement>\n+ <yield />\n+ </requirements>\n+ </xml>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1101/gr.209601.116</citation>\n+ <citation type="bibtex">\n+ @misc{githubUMI-tools,\n+ title = {UMI-tools},\n+ publisher = {GitHub},\n+ journal = {GitHub repository},\n+ url = {https://github.com/CGATOxford/UMI-tools},\n+ }\n+ </citation>\n+ </citations>\n+ </xml>\n+ <xml name="advanced_options_macro">\n+ <section name="advanced" title="Extra parameters" expanded="false">\n+ <param argument="--random-seed" type="integer" min="0" optional="true" label="Random Seed" />\n+ </section>\n+ </xml>\n+ <token name="@ADVANCED_OPTIONS@"><![CDATA[\n+ #if str($advanced.random_seed) != \'\'\n+ --random-seed=\'$advanced.random_seed\'\n+ #end if\n+ ]]></token>\n+ \n+ <!-- macros for extract and whitelist-->\n+ \n <macro name="barcode_sanitizer" >\n <sanitizer invalid_char="">\n <valid initial="string.letters,string.digits">\n@@ -23,90 +61,510 @@\n </valid>\n </sanitizer>\n </macro>\n- <macro name="barcode2_conditional" >\n- <conditional name="barcode">\n- <param name="barcode_select" argument="--split-barcode" type="select" label="Barcode on both reads?">\n- <option value="first_read_only">Barcode on first read only</option>\n- <option value="both_reads">Barcode on both reads</option>\n- </param>\n- <when value="first_read_only"/>\n- <when value="both_reads">\n- <param name="bc_pattern2" argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read"\n- help="Use this option to specify the format of the UMI/barcode for\n- the second read pair if required." >\n- <expand macro="barcode_sanitizer" />\n- </param>\n- </when>\n- </conditional>\n+ <xml name="sanitize_tag" >\n+ <sanitizer invalid_char="">\n+ <valid initial="string.letters,string.digits" />\n+ </sanitizer>\n+ </xml>\n+ <macro name="barcode1_macro" >\n+ <param argument="--bc-pattern" type="text" label="Barcode pattern for first read"\n+ help="Use this option to specify the format of the UMI/barcode. Use Ns to\n+ represent the random positions and Xs to indicate the bc positions.\n+ Bases with Ns will be extracted and added to the read name. Remaining\n+ bases, marked with an X will be reattached to the read">\n+ <validator type="empty_field" /> \n+ <expand macro="barcode_sanitizer" />\n+ </param>\n </macro>\n+ <macro name="barcode2_macro" >\n+ <param argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read"\n+ help="Use this option to specify the format of the UMI/barcode for\n+ the second read pair if required" >\n+ <expand macro="barcode_sanitizer" />\n+ </param>\n+ </macro>\n+ <!-- not just fastq because this would allow also fastqcsanger -->\n+ <token name="@FASTQ_FORMATS@">fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz</token>\n+ <xml name="bio_tools">\n+ <xrefs>\n+ <xref type="bio.tools">umi-tools</xref>\n+ </xrefs>\n+ </xml>\n <xml name="input_types">\n- <conditional name="in'..b'tag specified so you do not need to supply the mapping file">\n+ <expand macro="sanitize_tag" />\n+ </param>\n+ <param argument="--assigned-status-tag" type="text" optional="true" label="Bam tag describing whether read is assigned to a gene" help="By default, this is set as the same tag as --gene-tag">\n+ <expand macro="sanitize_tag" />\n+ </param>\n+ <param argument="--skip-tags-regex" name="skip_tags_regex" type="text" label="Skip any reads where the gene matches this tag" value="" >\n+ <expand macro="barcode_sanitizer" />\n+ </param>\n+ <param argument="--per-contig" type="boolean" truevalue="--per-contig" falsevalue="" label="Deduplicate per contig" help="Field 3 in BAM; RNAME. All reads with the same contig will be considered to have the same alignment position. This is useful if your library prep generates PCR duplicates with non identical alignment positions such as CEL-Seq. In this case, you would align to a reference transcriptome with one transcript per gene" />\n+ <param argument="--gene-transcript-map" type="data" format="tabular" optional="true" label="Tabular file mapping genes to transripts" />\n+ <param argument="--per-cell" name="per_cell" type="boolean" truevalue="--per-cell" falsevalue="" label="Group reads only if they have the same cell barcode" />\n+ </section>\n+ </xml>\n+ <token name="@SC_OPTIONS@"><![CDATA[\n+ #if str($sc.gene_tag) != "":\n+ --gene-tag \'$sc.gene_tag\'\n+ #end if\n+ #if str($sc.assigned_status_tag) != "":\n+ --assigned-status-tag \'$sc.assigned_status_tag\'\n+ #end if\n+ #if str($sc.skip_tags_regex) != "":\n+ --skip-tags-regex \'$sc.skip_tags_regex\'\n+ #end if\n+ $sc.per_contig\n+ #if $sc.gene_transcript_map:\n+ --gene-transcript-map \'$sc.gene_transcript_map\'\n+ #end if\n+ $sc.per_cell\n+ ]]></token>\n+\n+ <xml name="groupdedup_options_macro">\n+ <section name="gd" title="group/dedup specific options">\n+ <param argument="--buffer-whole-contig" type="boolean" truevalue="--buffer-whole-contig" falsevalue="" label="Read whole contig before outputting bundles" help="Guarantees that no reads are missed, but increases memory usage" />\n+ <!-- TODO this option is hidden on the CLI. Should we expose it? -->\n+ <param argument="--whole-contig" type="boolean" truevalue="--whole-contig" falsevalue="" label="Consider all alignments to a single contig together" help="This is useful if you have aligned to a transcriptome multi-fasta" />\n+ <param argument="--multimapping-detection-method" type="select" optional="true" label="BAM Tag indicating multimapping " help="Some aligners identify multimapping using bam tags. Setting this option to NH, X0 or XT will use these tags when selecting the best read amongst reads with the same position and umi">\n+ <option value="NH">NH</option>\n+ <option value="X0">X0</option>\n+ <option value="XT">XT</option>\n+ </param>\n+ </section>\n+ </xml>\n+ <token name="@GROUPDEDUP_OPTIONS@"><![CDATA[\n+ $gd.buffer_whole_contig\n+ $gd.whole_contig\n+ $gd.multimapping_detection_method\n+ ]]></token>\n+ \n+ <xml name="log_input_macro">\n+ <param argument="--log" type="boolean" label="Output log?" truevalue="--log" falsevalue="" help="Choose if you want to generate a text file containing logging information" />\n+ </xml>\n+ <xml name="log_output_macro">\n+ <data name="out_log" format="txt" label="${tool.name} on ${on_string}: logfile" >\n+ <filter>log</filter>\n+ </data>\n+ </xml>\n+ <token name="@LOG@"><![CDATA[\n+ #if $log:\n+ --log=\'$out_log\'\n+ #end if\n+ --log2stderr\n+ ]]></token>\n+\n </macros>\n' |
| b |
| diff -r 8250ea3a1501 -r e654095ab143 test-data/chr19_gene_tags.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chr19_gene_tags.sam Mon Sep 13 14:49:44 2021 +0000 |
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| b'@@ -0,0 +1,1492 @@\n+@HD\tVN:1.4\tSO:queryname\n+@SQ\tSN:chr1\tLN:248956422\n+@SQ\tSN:chr2\tLN:242193529\n+@SQ\tSN:chr3\tLN:198295559\n+@SQ\tSN:chr4\tLN:190214555\n+@SQ\tSN:chr5\tLN:181538259\n+@SQ\tSN:chr6\tLN:170805979\n+@SQ\tSN:chr7\tLN:159345973\n+@SQ\tSN:chr8\tLN:145138636\n+@SQ\tSN:chr9\tLN:138394717\n+@SQ\tSN:chr10\tLN:133797422\n+@SQ\tSN:chr11\tLN:135086622\n+@SQ\tSN:chr12\tLN:133275309\n+@SQ\tSN:chr13\tLN:114364328\n+@SQ\tSN:chr14\tLN:107043718\n+@SQ\tSN:chr15\tLN:101991189\n+@SQ\tSN:chr16\tLN:90338345\n+@SQ\tSN:chr17\tLN:83257441\n+@SQ\tSN:chr18\tLN:80373285\n+@SQ\tSN:chr19\tLN:58617616\n+@SQ\tSN:chr20\tLN:64444167\n+@SQ\tSN:chr21\tLN:46709983\n+@SQ\tSN:chr22\tLN:50818468\n+@SQ\tSN:chrX\tLN:156040895\n+@SQ\tSN:chrY\tLN:57227415\n+@SQ\tSN:chrM\tLN:16569\n+@SQ\tSN:GL000008.2\tLN:209709\n+@SQ\tSN:GL000009.2\tLN:201709\n+@SQ\tSN:GL000194.1\tLN:191469\n+@SQ\tSN:GL000195.1\tLN:182896\n+@SQ\tSN:GL000205.2\tLN:185591\n+@SQ\tSN:GL000208.1\tLN:92689\n+@SQ\tSN:GL000213.1\tLN:164239\n+@SQ\tSN:GL000214.1\tLN:137718\n+@SQ\tSN:GL000216.2\tLN:176608\n+@SQ\tSN:GL000218.1\tLN:161147\n+@SQ\tSN:GL000219.1\tLN:179198\n+@SQ\tSN:GL000220.1\tLN:161802\n+@SQ\tSN:GL000221.1\tLN:155397\n+@SQ\tSN:GL000224.1\tLN:179693\n+@SQ\tSN:GL000225.1\tLN:211173\n+@SQ\tSN:GL000226.1\tLN:15008\n+@SQ\tSN:KI270302.1\tLN:2274\n+@SQ\tSN:KI270303.1\tLN:1942\n+@SQ\tSN:KI270304.1\tLN:2165\n+@SQ\tSN:KI270305.1\tLN:1472\n+@SQ\tSN:KI270310.1\tLN:1201\n+@SQ\tSN:KI270311.1\tLN:12399\n+@SQ\tSN:KI270312.1\tLN:998\n+@SQ\tSN:KI270315.1\tLN:2276\n+@SQ\tSN:KI270316.1\tLN:1444\n+@SQ\tSN:KI270317.1\tLN:37690\n+@SQ\tSN:KI270320.1\tLN:4416\n+@SQ\tSN:KI270322.1\tLN:21476\n+@SQ\tSN:KI270329.1\tLN:1040\n+@SQ\tSN:KI270330.1\tLN:1652\n+@SQ\tSN:KI270333.1\tLN:2699\n+@SQ\tSN:KI270334.1\tLN:1368\n+@SQ\tSN:KI270335.1\tLN:1048\n+@SQ\tSN:KI270336.1\tLN:1026\n+@SQ\tSN:KI270337.1\tLN:1121\n+@SQ\tSN:KI270338.1\tLN:1428\n+@SQ\tSN:KI270340.1\tLN:1428\n+@SQ\tSN:KI270362.1\tLN:3530\n+@SQ\tSN:KI270363.1\tLN:1803\n+@SQ\tSN:KI270364.1\tLN:2855\n+@SQ\tSN:KI270366.1\tLN:8320\n+@SQ\tSN:KI270371.1\tLN:2805\n+@SQ\tSN:KI270372.1\tLN:1650\n+@SQ\tSN:KI270373.1\tLN:1451\n+@SQ\tSN:KI270374.1\tLN:2656\n+@SQ\tSN:KI270375.1\tLN:2378\n+@SQ\tSN:KI270376.1\tLN:1136\n+@SQ\tSN:KI270378.1\tLN:1048\n+@SQ\tSN:KI270379.1\tLN:1045\n+@SQ\tSN:KI270381.1\tLN:1930\n+@SQ\tSN:KI270382.1\tLN:4215\n+@SQ\tSN:KI270383.1\tLN:1750\n+@SQ\tSN:KI270384.1\tLN:1658\n+@SQ\tSN:KI270385.1\tLN:990\n+@SQ\tSN:KI270386.1\tLN:1788\n+@SQ\tSN:KI270387.1\tLN:1537\n+@SQ\tSN:KI270388.1\tLN:1216\n+@SQ\tSN:KI270389.1\tLN:1298\n+@SQ\tSN:KI270390.1\tLN:2387\n+@SQ\tSN:KI270391.1\tLN:1484\n+@SQ\tSN:KI270392.1\tLN:971\n+@SQ\tSN:KI270393.1\tLN:1308\n+@SQ\tSN:KI270394.1\tLN:970\n+@SQ\tSN:KI270395.1\tLN:1143\n+@SQ\tSN:KI270396.1\tLN:1880\n+@SQ\tSN:KI270411.1\tLN:2646\n+@SQ\tSN:KI270412.1\tLN:1179\n+@SQ\tSN:KI270414.1\tLN:2489\n+@SQ\tSN:KI270417.1\tLN:2043\n+@SQ\tSN:KI270418.1\tLN:2145\n+@SQ\tSN:KI270419.1\tLN:1029\n+@SQ\tSN:KI270420.1\tLN:2321\n+@SQ\tSN:KI270422.1\tLN:1445\n+@SQ\tSN:KI270423.1\tLN:981\n+@SQ\tSN:KI270424.1\tLN:2140\n+@SQ\tSN:KI270425.1\tLN:1884\n+@SQ\tSN:KI270429.1\tLN:1361\n+@SQ\tSN:KI270435.1\tLN:92983\n+@SQ\tSN:KI270438.1\tLN:112505\n+@SQ\tSN:KI270442.1\tLN:392061\n+@SQ\tSN:KI270448.1\tLN:7992\n+@SQ\tSN:KI270465.1\tLN:1774\n+@SQ\tSN:KI270466.1\tLN:1233\n+@SQ\tSN:KI270467.1\tLN:3920\n+@SQ\tSN:KI270468.1\tLN:4055\n+@SQ\tSN:KI270507.1\tLN:5353\n+@SQ\tSN:KI270508.1\tLN:1951\n+@SQ\tSN:KI270509.1\tLN:2318\n+@SQ\tSN:KI270510.1\tLN:2415\n+@SQ\tSN:KI270511.1\tLN:8127\n+@SQ\tSN:KI270512.1\tLN:22689\n+@SQ\tSN:KI270515.1\tLN:6361\n+@SQ\tSN:KI270516.1\tLN:1300\n+@SQ\tSN:KI270517.1\tLN:3253\n+@SQ\tSN:KI270518.1\tLN:2186\n+@SQ\tSN:KI270519.1\tLN:138126\n+@SQ\tSN:KI270521.1\tLN:7642\n+@SQ\tSN:KI270522.1\tLN:5674\n+@SQ\tSN:KI270528.1\tLN:2983\n+@SQ\tSN:KI270529.1\tLN:1899\n+@SQ\tSN:KI270530.1\tLN:2168\n+@SQ\tSN:KI270538.1\tLN:91309\n+@SQ\tSN:KI270539.1\tLN:993\n+@SQ\tSN:KI270544.1\tLN:1202\n+@SQ\tSN:KI270548.1\tLN:1599\n+@SQ\tSN:KI270579.1\tLN:31033\n+@SQ\tSN:KI270580.1\tLN:1553\n+@SQ\tSN:KI270581.1\tLN:7046\n+@SQ\tSN:KI270582.1\tLN:6504\n+@SQ\tSN:KI270583.1\tLN:1400\n+@SQ\tSN:KI270584.1\tLN:4513\n+@SQ\tSN:KI270587.1\tLN:2969\n+@SQ\tSN:KI270588.1\tLN:6158\n+@SQ\tSN:KI270589.1\tLN:44474\n+@SQ\tSN:KI270590.1\tLN:4685\n+@SQ\tSN:KI270591.1\tLN:5796\n+@SQ\tSN:KI270593.1\tLN:3041\n+@SQ\tSN:KI270706.1\tLN:175055\n+@SQ\tSN:KI270707.1\tLN:32032\n+@SQ\tSN:KI270708.1\tLN:127682\n+@SQ\tSN:KI270709.1\tLN'..b'44:H5FCJBGXY:4:23606:6087:6093:CELL_ACAAGG:UMI_GCACAA:SAMPLE_CGATGT:UID_CGATGTACAAGGGCACAA\t16\tchr19\t647844\t255\t60M\t*\t0\t0\tTAATTTAAAATTATAAAAATCTTTCCACCGCTGAACGTTTAGAGGGTGAGGTTAGACAGA\t/<A<E<AAEE/AE6EEEEEAE/AEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA\tNH:i:1\tHI:i:1\tAS:i:59\tnM:i:0\tXF:Z:ENSG00000070423.17\n+NS500668:144:H5FCJBGXY:4:23606:19406:18847:CELL_ACAAGG:UMI_ACGTAT:SAMPLE_CGATGT:UID_CGATGTACAAGGACGTAT\t0\tchr19\t807553\t255\t60M\t*\t0\t0\tCCTTCCCCTTTCCCTATTTTTTTTCTTGCCCTGATCCGGAATTTCTTTGCCAACTGACTG\tAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEAEE/EEEEEEEEEEEEEEEEEEEEEA<AA/\tNH:i:1\tHI:i:1\tAS:i:59\tnM:i:0\tXF:Z:ENSG00000011304.18\n+NS500668:144:H5FCJBGXY:4:23606:22946:6130:CELL_ACAAGG:UMI_GCTAGG:SAMPLE_CGATGT:UID_CGATGTACAAGGGCTAGG\t0\tchr19\t812039\t255\t60M\t*\t0\t0\tTGTTGTGAGACCCGAGGGGCGGCGGCGCGGTTTTTTATGGTGACACAAATGTATATTTTG\tAAAAA//EEEEE<<E///EAEEEEEEEEEA/<E//EEE/E//EEEEEEEA/EEEEE/<A/\tNH:i:1\tHI:i:1\tAS:i:59\tnM:i:0\tXF:Z:ENSG00000011304.18\n+NS500668:144:H5FCJBGXY:4:23607:1822:13398:CELL_ACAAGG:UMI_GCCGAA:SAMPLE_CGATGT:UID_CGATGTACAAGGGCCGAA\t16\tchr19\t938931\t255\t13S47M\t*\t0\t0\tGCCAAAAAATGGTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTTGTTTTGTCACCCAGGC\t/<//EA/A////<AEEEEEEAEEEEEEEEEEEEEEEEEEE/EEEEEEEEE/EEEEAAAAA\tNH:i:1\tHI:i:1\tAS:i:46\tnM:i:0\tXF:Z:Unassigned_NoFeatures\n+NS500668:144:H5FCJBGXY:4:23607:10971:2167:CELL_ACAAGG:UMI_GCTAGG:SAMPLE_CGATGT:UID_CGATGTACAAGGGCTAGG\t0\tchr19\t812062\t255\t58M2S\t*\t0\t0\tGGCGCGCTTTTTTAAGGAGACACAAATATATATTTTGCTAACAGCAATTCCAAGCTCACA\t//A/A6/EEEEEEE/EE/E6EEEEEA//E/E///A/E<///</<6/E//A<E///<////\tNH:i:1\tHI:i:1\tAS:i:47\tnM:i:5\tXF:Z:ENSG00000011304.18\n+NS500668:144:H5FCJBGXY:4:23608:13283:1095:CELL_ACAAGG:UMI_AGTTTA:SAMPLE_CGATGT:UID_CGATGTACAAGGAGTTTA\t0\tchr19\t812062\t255\t60M\t*\t0\t0\tGGCGCCGTTTTTTATGGTGACACAAATGTATATTTTGCTAACAGCAATTCCATGCTCAGT\t//A/A6/E//E</AA//E/<E/E6EE///E/</A//E/AAA///EEAA/E/<////EA/<\tNH:i:1\tHI:i:1\tAS:i:55\tnM:i:2\tXF:Z:ENSG00000011304.18\n+NS500668:144:H5FCJBGXY:4:23609:5585:17562:CELL_ACAAGG:UMI_GCTAGG:SAMPLE_CGATGT:UID_CGATGTACAAGGGCTAGG\t0\tchr19\t812089\t255\t60M\t*\t0\t0\tGTATATTTTGCTAACAGCAATTCCAGGCTCAGTATTGTGACCGCGGAACCACAGGGGACC\tAAA/AA////E/EEE/EEEE//A/E//EEE6E/EE/</6/EA<//E//E/EEEA////A<\tNH:i:1\tHI:i:1\tAS:i:57\tnM:i:1\tXF:Z:ENSG00000011304.18\n+NS500668:144:H5FCJBGXY:4:23611:19058:11533:CELL_TTCACG:UMI_GCCTTA:SAMPLE_CGATGT:UID_CGATGTTTCACGGCCTTA\t0\tchr19\t811797\t255\t60M\t*\t0\t0\tCCTGCAGTCGCCTAGAAAACTTGCTCTCAAACTTCAGGGTTTTTTCTTCCTTCAAATTTT\tAAAAAEEEEAEEAEEEE/AEEEEE/EE/EA/EEAAEEEEEEEAEEEEEE<<AEEEEEEEE\tNH:i:1\tHI:i:1\tAS:i:59\tnM:i:0\tXF:Z:ENSG00000011304.18\n+NS500668:144:H5FCJBGXY:4:23611:23053:18525:CELL_ACAAGG:UMI_CCAGCA:SAMPLE_CGATGT:UID_CGATGTACAAGGCCAGCA\t0\tchr19\t812062\t255\t60M\t*\t0\t0\tGGCGCGGTTTTTTATTTTTACAAAAATTTATATTTTGCTAACAGCAATTCCAGGCTCAGT\t/AA/A6E/E/EEE/E//E6////AAEE6E/EEEEEAE////AEAEEEAEE/E/AEEE<EE\tNH:i:1\tHI:i:1\tAS:i:49\tnM:i:5\tXF:Z:ENSG00000011304.18\n+NS500668:144:H5FCJBGXY:4:23611:23963:1840:CELL_TTCACG:UMI_GCTTTT:SAMPLE_CGATGT:UID_CGATGTTTCACGGCTTTT\t16\tchr19\t647540\t255\t50M10S\t*\t0\t0\tAGTGTATTTTAAATAGCTTTCAAGATACACATATTTTTTCCTTTAAAAAAAAAGTCTGGT\t/EE<E/EEE//EAEEA<EEE//EEEEEEAEAEEEEEE/E6EEEEEEEEEEAEEEEAAAAA\tNH:i:1\tHI:i:1\tAS:i:49\tnM:i:0\tXF:Z:ENSG00000070423.17\n+NS500668:144:H5FCJBGXY:4:23612:8565:12159:CELL_ACAAGG:UMI_ACATAG:SAMPLE_CGATGT:UID_CGATGTACAAGGACATAG\t0\tchr19\t812062\t255\t2S58M\t*\t0\t0\tAGGGCGCGGTTTTTTATGGTGACACAAATGTATATTTTGCTAACAGCAATTCCAGGCTCA\tA///A/AE/E/E//E/EEE/EEAEEEEEAEEAE/AAA/66EEEEEA<EE/<AEAE/E/AE\tNH:i:1\tHI:i:1\tAS:i:57\tnM:i:0\tXF:Z:ENSG00000011304.18\n+NS500668:144:H5FCJBGXY:4:23612:14819:6245:CELL_TTCACG:UMI_CTCATT:SAMPLE_CGATGT:UID_CGATGTTTCACGCTCATT\t0\tchr19\t994331\t255\t60M\t*\t0\t0\tGGCCGGCCAAGTGAGGCCCGGAGACCCCGGCCCGAGGCGCCCAGGCCTGAGCCCCATGCC\tAAAAAEEEEEEEE/EEEEEEE/E/EEEAE<EEAE<</6EEEE/</<EE/AAAEEA<A/<A\tNH:i:1\tHI:i:1\tAS:i:59\tnM:i:0\tXF:Z:ENSG00000065268.10\n+NS500668:144:H5FCJBGXY:4:23612:25822:12295:CELL_TTCACG:UMI_GATTGT:SAMPLE_CGATGT:UID_CGATGTTTCACGGATTGT\t0\tchr19\t812059\t255\t60M\t*\t0\t0\tGGCGGCGCGGTTTTTTATGGTGACACAAATGTATATTTTGCTAACAGCAATTCCAGGCTC\tAAAAAEEEEEEEEEEEEEEEEEAEEEAAAEAEAE/EE//AEA/EEEEEEEEAE6A<<AA<\tNH:i:1\tHI:i:1\tAS:i:59\tnM:i:0\tXF:Z:ENSG00000011304.18\n' 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| diff -r 8250ea3a1501 -r e654095ab143 test-data/group_in2.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/group_in2.sam Mon Sep 13 14:49:44 2021 +0000 |
| b |
| b'@@ -0,0 +1,403 @@\n+@HD\tVN:1.0\tSO:coordinate\n+@SQ\tSN:chrM\tLN:17009\n+@PG\tID:hisat2\tPN:hisat2\tVN:2.0.5\tCL:"/var/galaxy/tool_dependencies/_conda/envs/mulled-v1-2bb67013a57cac1e35f407d06d1f347baae35159f498496f1e36f84784069212/bin/hisat2-align-s --wrapper basic-0 -p 4 -x genome -1 input_f.fastq -2 input_r.fastq"\n+chrM_111_723_3:2:0_4:1:0_c3/1_CT\t163\tchrM\t114\t60\t1S197M\t=\t524\t611\tCGACTCAGTCAAATATGTGGTTGCTGGGCTTATTCTCTATGCGGGTTCTCCACACGCACAGACAGTCAGGGTGCTATTCAGTCAATGGTCACAGGACATATACTTAAATTCCTATTGTTCCACAGGACACGGGATGCGCGCACCCAGGTTTGCGTGCACACGTGTACACGTACACACGTAGACACGTACACACGTACA\t222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-16\tZS:i:-28\tXN:i:0\tXM:i:5\tXO:i:0\tXG:i:0\tNM:i:5\tMD:Z:15A1T26G100C33C17\tYS:i:-15\tYT:Z:CP\tNH:i:1\n+chrM_513_1000_4:1:0_4:2:0_60/1_GT\t163\tchrM\t516\t60\t1S197M\t=\t801\t486\tCACACACGTGTACACGTACACACGTACACACGTACACACGTACACACTTATCCACGCGAACGCTTTAATTTAAGTAAATAACTCGCTTAATCAAACCCCCCTTACCCCCCGTTAACCTTATTTCTAATAATACGTGCCTATTTATGTCTTGCCCAACCCCACAAACAAGACTAGACCGTACCTAAATATAAGGCCTAA\t222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-16\tXN:i:0\tXM:i:5\tXO:i:0\tXG:i:0\tNM:i:5\tMD:Z:46G3A31A39A29A44\tYS:i:-18\tYT:Z:CP\tNH:i:1\n+chrM_518_1106_2:1:0_5:2:0_44/1_CA\t163\tchrM\t520\t60\t198M\t=\t907\t587\tACGTGTACACGTACACACTTACACACGTACACACGTACACACTTATACACGCGAACGCTTTAATTTAAGTAAATAACTAGCTTAATCAAACCCCCCTTACCCCCCGTAAACCTTATTTATAATAATACGTGCCTATTTATGTCTTGCCAAACCCCACAAACAAGACTAGACCGTACCTAAATATAAGGCCTAAGAAAA\t222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-9\tXN:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tNM:i:3\tMD:Z:18G23G64T90\tYS:i:-21\tYT:Z:CP\tNH:i:1\n+chrM_111_723_3:2:0_4:1:0_c3/2_CT\t83\tchrM\t524\t60\t200M\t=\t114\t-611\tGTACACGTACACACGTACACACGTACACACGTACACACTTATACACCCGAACGCTTTATTTTAAGTAAATAACTAGCTTAATCAAACCCCCCTTACCCCCCGTTAACCTTATTTATAATAATACGTGCCTATTTATGTCTTGCCAAACCCCACAAACAAGACTAGACCGTACCTAAATATTAGGCCTAAGATAACGCTTA\t22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-15\tXN:i:0\tXM:i:5\tXO:i:0\tXG:i:0\tNM:i:5\tMD:Z:38G7G11A121A10A8\tYS:i:-16\tYT:Z:CP\tNH:i:1\n+chrM_578_1113_4:1:0_4:2:0_19/1_TT\t163\tchrM\t580\t60\t198M\t=\t914\t534\tTAATTTAAGTAAATAACTAGCTTAATCAAACCCCCCTTACCCCCCGTTAACCTTATTTATAATAATCCGTGCCTATTTATGTCTTGCCAAACCCCACAAACAAGACTAGACCGTACCTAAATATAAGGCCTACGAAAACGCTTATAAGCTTACCAATCCCCTATTATTACTAGCTACTACGCCTAAATCATAACTCTG\t222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-15\tZS:i:-24\tXN:i:0\tXM:i:5\tXO:i:0\tXG:i:0\tNM:i:5\tMD:Z:66A65A46A0T0A16\tYS:i:-18\tYT:Z:CP\tNH:i:1\n+chrM_637_1116_4:2:0_2:5:0_8f/2_AT\t99\tchrM\t637\t60\t200M\t=\t917\t478\tTATCATAATACGTGCCTATTTATGTCATGCCAAACCCCACAAACAAGACTAGACCGTACCTAAATATAAGGCCTAAGACAACGCTTATAAGCTTACCAATCCCCTATTATTACTAGCTACTAAGCCTAAATCATAACTCTGTTCGCAGTTATCTATAGATATACCGACCTGACTCTAATTCGACCCTATCGAACAACATT\t22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-18\tZS:i:-19\tXN:i:0\tXM:i:6\tXO:i:0\tXG:i:0\tNM:i:6\tMD:Z:3A22T51A44T0A57T17\tYS:i:-21\tYT:Z:CP\tNH:i:1\n+chrM_513_1000_4:1:0_4:2:0_60/2_GT\t83\tchrM\t801\t60\t200M\t=\t516\t-486\tCGACCTGACTCTAATTCGTCCCTATCGAACAACATTTTACATGTCTACGTTAGCACCACATCCCAGTTAATGTAGCGTAAACCTATAAAGCAAGGCACTGAAAATGCCTAGATGAGTAGCCAGACTCCATAAACACAAAAGTTTGGTCCTGGCCTTTCCATTAGTTATTAATAAGATTACACATGCAAGCCTCCGCAGCC\t22222222222222222222222222222222222222222222222222222222222222222222'..b'TACATAAGACATACTATGTATATCGTGCATTAATTGCTAGTCCCCATAAATATTAAGCATGTACAGTAGTTTATATATATTACATAAGACATAATAGTGCTTAATCGGGCATTCACCTTAATTCTAGGACAGTCTTCTATGGAACTCAACTATTCCAAAGAT\t222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-16\tZS:i:-36\tXN:i:0\tXM:i:5\tXO:i:0\tXG:i:0\tNM:i:5\tMD:Z:18A6T57G59T35C17\tYS:i:-15\tYT:Z:CP\tNH:i:1\n+chrM_16373_16837_7:2:0_4:1:0_9/2_GT\t83\tchrM\t16638\t60\t200M\t=\t16375\t-463\tATTAAGCATGTACAGTAGTTTATATATATTACATAACACATACTATGTATTTCGTGCATTAATTGCTAGTCCCAATAAATATTAAGCATGTACAGTTGTTTATATATATTACATAAGACATAATAGTGCTTAATCGTGCATTCACCTTAATTCTAGGACAGTCTTCTATGGACCTCAACTATTCCAAAGAGCTTAATCAC\t22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-15\tXN:i:0\tXM:i:5\tXO:i:0\tXG:i:0\tNM:i:5\tMD:Z:36G13A22C2G19A103\tYS:i:-27\tYT:Z:CP\tNH:i:1\n+chrM_16363_16864_3:2:1_3:2:0_ba/2_TA\t83\tchrM\t16665\t60\t200M\t=\t16365\t-500\tATTACATAAGACATACTATGTATATCGTACATTAATTGCTAGTCCCCATAAATATTAAGCATGTACAGTAGTTTATATATATTAAATAAGACATAATAGTGCTTTATAGTGCATTCACCTTAATTCTAGGACAGTCTTCTATGGACCTCAACTATTCCAAAGAGCTTAATCACCTGGCCTCGAGAAACCAGCAATCCTTG\t22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-15\tXN:i:0\tXM:i:5\tXO:i:0\tXG:i:0\tNM:i:5\tMD:Z:28G20G34C19A2C92\tYS:i:-23\tYT:Z:CP\tNH:i:1\n+chrM_16484_16992_6:0:0_3:0:0_2c/1_AG\t147\tchrM\t16793\t60\t198M\t=\t16484\t-507\tGGACAGTCTTCTATGGACCTCAACGATTCCAAAGAGCTTAATCACCTGGCCTCGAGAAACCAGCAATCCTTGCTCGAACGTGTACCTCTTCTCGCTCCGGGCCCATTTCAACGTGGGGGTTTCTATAACGGAACTATAACTGGCATATGGTTCTTACTTCAGGGCCATAAAATCCTTGAAACCAATCCTTCAGTTCTC\t222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-9\tXN:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tNM:i:3\tMD:Z:24T113C7C51\tYS:i:-18\tYT:Z:CP\tNH:i:1\n+chrM_12782_13288_5:1:0_6:0:0_3/2_TA\t77\t*\t0\t0\t*\t*\t0\t0\tCAACTATAATATTTATCTCCTCAGGAGAACAAGCAATTATCTCAAACTGACACTGACTATCAATCCAAACTCTCAAGCTATCACTAAGCTTTAAAATAGATTAATTCTCAACCATCATTATCCGTGTAGCGCTTTTCGTCACATGGTCCATCATAGAATTCTCAATGTGGTACATGCACTCCGACCCATACATCAACCGA\t22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n+chrM_12782_13288_5:1:0_6:0:0_3/1_TA\t141\t*\t0\t0\t*\t*\t0\t0\tCATCGAAGCCCTAGTAATGGAATATTTAGGTTCTCGTGTTGGGTGATAAAGATTTGTTGGAAGTCCCATGCGTTTGAGTTGGTTAGAAATCCTGCTATGGCTATGATTAAGCCTACGTCTCCAATTCGGTTGTAGAGGATTGCTTGTAGGGCGGCAGTGTTTGCATCTGCTCGGCCATATCATCATCCGATAAGTCGA\t222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n+chrM_15422_15911_4:2:0_5:1:0_99/2_GA\t77\t*\t0\t0\t*\t*\t0\t0\tATGGGATACGTCCTGCCATGAGGCCAAATGTCCTTCTGAGGAGCAACGGTAATCCCTAACCTGCTGTCAGCAATTCCATACCTCGGGACTGAACTAGTAGAATGAATCTGAGGGGGGTTCTCAGTAGACAAAGCCACCCTAACACGATTCTTTGGCTTCCACTTCATTCTTTCATTCATTATCTCAGCCTTAGCAGGAGT\t22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n+chrM_15422_15911_4:2:0_5:1:0_99/1_GA\t141\t*\t0\t0\t*\t*\t0\t0\tGCTGCCCCTAGTTTGTTAGGGATGGATCGGAGAATTGCGTATGCGAATAGGAAGTATCATTCAGGTTAAATATGGGGAGGTGAATTTAAAGGGTTGGCTGGGATGTAGTTGTGTGGGTCTCCTAGCAGGTCTGGTGAAAATAGGACGAGTAGTATGAGTGTTAAAACTAGTACTAGAAGACCTAGGATTTCTTTGATT\t222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n' |
| b |
| diff -r 8250ea3a1501 -r e654095ab143 test-data/group_out4.bam |
| b |
| Binary file test-data/group_out4.bam has changed |
| b |
| diff -r 8250ea3a1501 -r e654095ab143 test-data/group_out4.tab --- a/test-data/group_out4.tab Wed Feb 10 19:29:55 2021 +0000 +++ b/test-data/group_out4.tab Mon Sep 13 14:49:44 2021 +0000 |
| b |
| b'@@ -0,0 +1,498 @@\n+read_id\tcontig\tposition\tgene\tumi\tumi_count\tfinal_umi\tfinal_umi_count\tunique_id\n+chrM_81_583_3:0:0_2:0:0_f4/1_TT\tchrM\t80\tNA\tTT\t1\tTT\t1\t0\n+chrM_110_732_3:0:0_2:0:0_160/1_CC\tchrM\t109\tNA\tCC\t1\tCC\t1\t1\n+chrM_118_613_6:0:0_4:0:0_169/1_AG\tchrM\t117\tNA\tAG\t1\tAG\t1\t2\n+chrM_149_684_2:0:0_2:0:0_6e/1_TA\tchrM\t148\tNA\tTA\t1\tTA\t1\t3\n+chrM_152_616_6:0:0_2:0:0_84/1_GC\tchrM\t151\tNA\tGC\t1\tGC\t1\t4\n+chrM_247_748_8:0:0_1:0:0_1b7/1_GC\tchrM\t246\tNA\tGC\t1\tGC\t1\t5\n+chrM_280_772_1:0:0_9:0:0_31/1_CG\tchrM\t279\tNA\tCG\t1\tCG\t1\t6\n+chrM_292_819_2:0:0_1:0:0_18d/1_CA\tchrM\t291\tNA\tCA\t1\tCA\t1\t7\n+chrM_390_890_3:0:0_6:0:0_bf/1_CA\tchrM\t389\tNA\tCA\t1\tCA\t1\t8\n+chrM_447_921_2:0:0_3:0:0_1cc/1_AC\tchrM\t446\tNA\tAC\t1\tAC\t1\t9\n+chrM_469_983_2:0:0_1:0:0_121/1_AC\tchrM\t468\tNA\tAC\t1\tAC\t1\t10\n+chrM_541_1074_3:0:0_8:1:0_22/1_AC\tchrM\t540\tNA\tAC\t1\tAC\t1\t11\n+chrM_8_556_3:0:0_2:0:0_1b1/1_AC\tchrM\t556\tNA\tAC\t1\tAC\t1\t12\n+chrM_112_577_2:0:0_4:0:0_17b/1_CG\tchrM\t577\tNA\tCG\t1\tCG\t1\t13\n+chrM_627_1063_6:0:0_4:1:0_12a/1_AA\tchrM\t626\tNA\tAA\t1\tAA\t1\t14\n+chrM_164_650_5:0:0_3:0:0_164/1_AC\tchrM\t650\tNA\tAC\t1\tAC\t1\t15\n+chrM_200_695_6:0:0_2:0:0_5a/1_TA\tchrM\t695\tNA\tTA\t3\tTA\t3\t16\n+chrM_168_695_5:0:0_2:0:0_1af/1_TA\tchrM\t695\tNA\tTA\t3\tTA\t3\t16\n+chrM_170_695_1:0:0_6:0:0_1e3/1_TA\tchrM\t695\tNA\tTA\t3\tTA\t3\t16\n+chrM_209_705_3:0:0_2:0:0_1b3/1_TA\tchrM\t705\tNA\tTA\t1\tTA\t1\t17\n+chrM_288_807_3:0:0_5:0:0_8e/1_AG\tchrM\t807\tNA\tAG\t1\tAG\t1\t18\n+chrM_818_1274_1:1:0_4:0:0_124/1_TC\tchrM\t817\tNA\tTC\t1\tTC\t1\t19\n+chrM_442_872_4:0:0_6:0:0_146/1_AT\tchrM\t872\tNA\tAT\t1\tAT\t1\t20\n+chrM_460_919_3:0:0_1:0:0_0/1_GA\tchrM\t919\tNA\tGA\t1\tGA\t1\t21\n+chrM_384_950_5:0:0_2:0:0_34/1_GG\tchrM\t950\tNA\tGG\t1\tGG\t1\t22\n+chrM_476_980_5:0:0_2:0:0_133/1_TA\tchrM\t980\tNA\tTA\t1\tTA\t1\t23\n+chrM_552_999_4:0:0_5:0:0_bb/1_AT\tchrM\t999\tNA\tAT\t1\tAT\t1\t24\n+chrM_512_1030_5:0:0_7:1:0_a5/1_AC\tchrM\t1030\tNA\tAC\t1\tAC\t1\t25\n+chrM_1103_1634_5:0:0_3:0:0_36/1_TA\tchrM\t1102\tNA\tTA\t1\tTA\t1\t26\n+chrM_648_1148_3:0:0_3:1:0_1d1/1_TT\tchrM\t1148\tNA\tTT\t1\tTT\t1\t27\n+chrM_1167_1797_8:0:0_2:1:0_14e/1_GT\tchrM\t1166\tNA\tGT\t1\tGT\t1\t28\n+chrM_619_1169_3:0:0_5:1:0_33/1_CC\tchrM\t1169\tNA\tCC\t1\tCC\t1\t29\n+chrM_668_1248_0:0:0_4:0:0_fa/1_TT\tchrM\t1248\tNA\tTT\t1\tTT\t1\t30\n+chrM_1288_1759_4:0:0_2:1:0_a1/1_TA\tchrM\t1287\tNA\tTA\t1\tTA\t1\t31\n+chrM_1327_1786_4:0:0_3:1:0_1ad/1_CA\tchrM\t1326\tNA\tCA\t1\tCA\t1\t32\n+chrM_866_1351_5:1:0_6:0:0_1c9/1_TA\tchrM\t1351\tNA\tTA\t1\tTA\t1\t33\n+chrM_853_1366_6:1:0_4:0:0_13b/1_TC\tchrM\t1366\tNA\tTC\t1\tTC\t1\t34\n+chrM_1399_1851_2:0:0_11:1:0_85/1_AT\tchrM\t1398\tNA\tAT\t1\tAT\t1\t35\n+chrM_946_1444_4:1:0_6:0:0_113/1_TT\tchrM\t1444\tNA\tTT\t1\tTT\t1\t36\n+chrM_943_1485_2:1:0_5:0:0_1e2/1_AT\tchrM\t1485\tNA\tAT\t1\tAT\t1\t37\n+chrM_1022_1501_4:0:0_5:0:0_132/1_GA\tchrM\t1501\tNA\tGA\t1\tGA\t1\t38\n+chrM_1504_2013_4:1:0_3:0:0_10b/1_AT\tchrM\t1503\tNA\tAT\t1\tAT\t1\t39\n+chrM_1505_1934_1:1:0_5:0:0_157/1_TC\tchrM\t1504\tNA\tTC\t1\tTC\t1\t40\n+chrM_997_1511_2:1:0_1:0:0_1d8/1_AT\tchrM\t1511\tNA\tAT\t1\tAT\t1\t41\n+chrM_1521_2070_5:1:0_3:0:0_1a/1_TA\tchrM\t1520\tNA\tTA\t1\tTA\t1\t42\n+chrM_1575_2126_5:1:0_2:1:0_18c/1_TA\tchrM\t1574\tNA\tTA\t1\tTA\t1\t43\n+chrM_1063_1598_5:0:0_5:0:0_f5/1_TG\tchrM\t1598\tNA\tTG\t1\tTG\t1\t44\n+chrM_1605_2128_3:1:0_4:1:0_1ea/1_TT\tchrM\t1604\tNA\tTT\t1\tTT\t1\t45\n+chrM_1065_1609_3:0:0_5:0:0_18e/1_TA\tchrM\t1609\tNA\tTA\t1\tTA\t1\t46\n+chrM_1140_1619_1:0:0_4:0:0_74/1_TT\tchrM\t1619\tNA\tTT\t1\tTT\t1\t47\n+chrM_1111_1626_4:0:0_2:0:0_186/1_AC\tchrM\t1626\tNA\tAC\t1\tAC\t1\t48\n+chrM_1664_2135_0:1:0_3:1:0_179/1_TT\tchrM\t1663\tNA\tTT\t1\tTT\t1\t49\n+chrM_1699_2147_1:0:0_7:0:0_10c/1_AA\tchrM\t1698\tNA\tAA\t1\tAA\t1\t50\n+chrM_1706_2240_3:0:0_6:0:0_99/1_GT\tchrM\t1705\tNA\tGT\t1\tGT\t1\t51\n+chrM_1756_2309_0:0:0_3:0:0_c3/1_AT\tchrM\t1755\tNA\tAT\t1\tAT\t1\t52\n+chrM_1344_1758_4:0:0_3:1:0_75/1_TT\tchrM\t1758\tNA\tTT\t1\tTT\t1\t53\n+chrM_1223_1777_5:0:0_6:1:0_42/1_TG\tchrM\t1777\tNA\tTG\t1\tTG\t1\t54\n+chrM_1790_2351_4:0:0_4:0:0_f3/1_CC\tchrM\t1789\tNA\tCC\t1\tCC\t1\t55\n+chrM_1308_1807_4:0:0_4:1:0_45/1_TA\tchrM\t1807\tNA\tTA\t1\tTA\t1\t56\n+chrM_1814_2315_6:0:0_3:0:0_12d/1_AA\tchrM\t1813\tNA\tAA\t1\tAA\t1\t57\n+chrM_1862_2304_4:0:0_1:0:0_19d/1_AA\tchrM\t1861\tNA\tAA\t1\tAA\t1\t58\n+chrM_1363_1869_5:0:0_3:1:0_aa/1_TA\tchrM\t1869\tNA\tTA\t1\tTA\t1\t59\n+chrM_1363_1887_2:0:0_3:0:0_d3/1_CA\tchrM\t1887\tNA\tCA\t1\tCA\t1\t60\n+chrM_1428_1904_7:0:0_1:0:0_1b0/1_AC\tchrM\t1904\tNA\tAC\t1\tAC\t1\t6'..b'\tTA\t1\t431\n+chrM_14135_14581_5:0:0_5:0:0_1de/1_AT\tchrM\t14581\tNA\tAT\t1\tAT\t1\t432\n+chrM_14612_15169_2:0:0_5:0:0_e4/1_TT\tchrM\t14611\tNA\tTT\t1\tTT\t1\t433\n+chrM_14668_15109_2:0:0_3:0:0_3d/1_TG\tchrM\t14667\tNA\tTG\t1\tTG\t1\t434\n+chrM_14696_15126_2:0:0_2:0:0_a7/1_AA\tchrM\t14695\tNA\tAA\t1\tAA\t1\t435\n+chrM_14727_15156_4:0:0_4:0:0_178/1_GA\tchrM\t14726\tNA\tGA\t1\tGA\t1\t436\n+chrM_14245_14783_3:0:0_1:0:0_9d/1_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' |
| b |
| diff -r 8250ea3a1501 -r e654095ab143 test-data/out_wl_paired.log --- a/test-data/out_wl_paired.log Wed Feb 10 19:29:55 2021 +0000 +++ b/test-data/out_wl_paired.log Mon Sep 13 14:49:44 2021 +0000 |
| b |
| @@ -1,14 +1,20 @@ -# output generated by whitelist --bc-pattern=CCCNNNNNNNNXXXXX --subset-reads=0 --stdin=/tmp/tmpibtvD6/files/000/dataset_5.dat --read2-in=/tmp/tmpibtvD6/files/000/dataset_6.dat --expect-cells=5 --error-correct-threshold=3 --method=reads --plot-prefix=OUT --log=/tmp/tmpibtvD6/files/000/dataset_8.dat -# job started at Sun Feb 25 10:50:16 2018 on bag -- e78e4e5b-e99e-426a-8a92-c8b3beeadf18 -# pid: 2385, system: Linux 4.13.0-32-generic #35-Ubuntu SMP Thu Jan 25 09:13:46 UTC 2018 x86_64 +# UMI-tools version: 1.1.2 +# output generated by whitelist --bc-pattern=CCCNNNNNNNNXXXXX --extract-method=string --subset-reads=0 --knee-method=density --stdin=input_read1.gz --read2-in=input_read2.gz --expect-cells=5 --error-correct-threshold=3 --method=reads --plot-prefix=OUT --log=/tmp/tmpcx2d26we/files/0/0/8/dataset_008b1843-bfa2-44fb-9d3c-52695bd9ce74.dat --log2stderr +# job started at Tue Jul 13 15:21:12 2021 on MOLSYB009 -- ba3841c0-b2d5-4188-88ca-4ee241163293 +# pid: 1155608, system: Linux 5.4.0-74-generic #83-Ubuntu SMP Sat May 8 02:35:39 UTC 2021 x86_64 +# allow_threshold_error : False # blacklist_tsv : None # cell_number : False # compresslevel : 6 +# ed_above_threshold : None # error_correct_threshold : 3 # expect_cells : 5 # extract_method : string -# filter_cell_barcodes : False -# log2stderr : False +# filtered_out : None +# filtered_out2 : None +# ignore_suffix : False +# knee_method : density +# log2stderr : True # loglevel : 1 # method : reads # pattern : CCCNNNNNNNNXXXXX @@ -16,25 +22,31 @@ # plot_prefix : OUT # prime3 : None # random_seed : None -# read2_in : /tmp/tmpibtvD6/files/000/dataset_6.dat +# read2_in : input_read2.gz # short_help : None -# stderr : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='UTF-8'> -# stdin : <_io.TextIOWrapper name='/tmp/tmpibtvD6/files/000/dataset_5.dat' mode='r' encoding='UTF-8'> -# stdlog : <_io.TextIOWrapper name='/tmp/tmpibtvD6/files/000/dataset_8.dat' mode='a' encoding='UTF-8'> -# stdout : <_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'> +# stderr : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='utf-8'> +# stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'> +# stdlog : <_io.TextIOWrapper name='/tmp/tmpcx2d26we/files/0/0/8/dataset_008b1843-bfa2-44fb-9d3c-52695bd9ce74.dat' mode='a' encoding='UTF-8'> +# stdout : <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'> # subset_reads : 0 # timeit_file : None # timeit_header : None # timeit_name : all +# tmpdir : None # whitelist_tsv : None -2018-02-25 10:50:16,016 INFO Starting barcode extraction -2018-02-25 10:50:16,017 INFO Parsed 0 reads -2018-02-25 10:50:16,019 INFO Starting - whitelist determination -2018-02-25 10:50:17,208 INFO Finished - whitelist determination -2018-02-25 10:50:17,208 INFO Starting - finding putative error cell barcodes -2018-02-25 10:50:17,208 INFO Finished - finding putative error cell barcodes -2018-02-25 10:50:17,208 INFO Writing out whitelist -2018-02-25 10:50:17,208 INFO Parsed 100 reads -2018-02-25 10:50:17,208 INFO 100 reads matched the barcode pattern -2018-02-25 10:50:17,208 INFO Found 23 unique cell barcodes -# job finished in 1 seconds at Sun Feb 25 10:50:17 2018 -- 2.35 0.08 0.00 0.00 -- e78e4e5b-e99e-426a-8a92-c8b3beeadf18 +2021-07-13 15:21:12,587 INFO Starting barcode extraction +2021-07-13 15:21:12,588 INFO Parsed 0 reads +2021-07-13 15:21:12,590 INFO Starting - whitelist determination +2021-07-13 15:21:14,249 INFO Finished - whitelist determination +2021-07-13 15:21:14,249 INFO Starting - finding putative error cell barcodes +2021-07-13 15:21:14,249 INFO building bktree +2021-07-13 15:21:14,249 INFO done building bktree +2021-07-13 15:21:14,249 INFO Finished - finding putative error cell barcodes +2021-07-13 15:21:14,249 INFO Top 1 cell barcodes passed the selected threshold +2021-07-13 15:21:14,249 INFO Writing out whitelist +2021-07-13 15:21:14,249 INFO Parsed 100 reads +2021-07-13 15:21:14,249 INFO 100 reads matched the barcode pattern +2021-07-13 15:21:14,249 INFO Found 23 unique cell barcodes +2021-07-13 15:21:14,249 INFO Found 15 total reads matching the selected cell barcodes +2021-07-13 15:21:14,249 INFO Found 85 total reads which can be error corrected to the selected cell barcodes +# job finished in 1 seconds at Tue Jul 13 15:21:14 2021 -- 7.19 0.62 0.08 0.02 -- ba3841c0-b2d5-4188-88ca-4ee241163293 |
| b |
| diff -r 8250ea3a1501 -r e654095ab143 umi-tools_counts.xml --- a/umi-tools_counts.xml Wed Feb 10 19:29:55 2021 +0000 +++ b/umi-tools_counts.xml Mon Sep 13 14:49:44 2021 +0000 |
| [ |
| b'@@ -1,115 +1,44 @@\n-<tool id="umi_tools_count" name="UMI-tools count" version="@VERSION@.1">\n+<tool id="umi_tools_count" name="UMI-tools count" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n <description>performs quantification of UMIs from BAM files</description>\n+ <expand macro="bio_tools"/>\n <macros>\n <import>macros.xml</import>\n- <xml name="sanitize_tag" >\n- <sanitizer invalid_char="">\n- <valid initial="string.letters,string.digits" />\n- </sanitizer>\n- </xml>\n </macros>\n <expand macro="requirements">\n+ <!-- TODO see comment in LINK_SAM_BAM_INPUT -->\n+ <requirement type="package" version="1.12">samtools</requirement>\n <requirement type="package" version="4.7">sed</requirement>\n </expand>\n <command detect_errors="exit_code"><![CDATA[\n-#import re\n-\n-ln -s \'${input_bam}\' \'input.bam\' &&\n-ln -s \'${input_bam.metadata.bam_index}\' \'input.bam.bai\' &&\n+ #import re\n+ @LINK_SAM_BAM_INPUT@ \n \n-umi_tools count\n- -I input.bam\n- \'$paired\'\n- --extract-umi-method=\'$barcodes.extract_umi_method.value\'\n-#if str($barcodes.extract_umi_method) == \'read_id\':\n- --umi-separator=\'$barcodes.umi_separator.value\'\n-#else if str($barcodes.extract_umi_method) == \'tag\':\n- --umi-tag=\'$barcodes.umi_tag.value\'\n- --cell-tag=\'$barcodes.cell_tag.value\'\n-#end if\n- --method=\'$method.value\'\n- --edit-distance-threshold=\'$edit_distance_threshold\'\n- --mapping-quality=\'$advanced.mapping_quality\'\n- --per-gene\n- \'$wide_format_cell_counts\'\n- \'$advanced.per_contig\'\n- \'$advanced.per_cell\'\n-\n-#if str($advanced.gene_tag) != "":\n- --gene-tag=\'$advanced.gene_tag.value\'\n-#end if\n-#if str($advanced.skip_tags_regex) != "":\n- --skip-tags-regex=\'$advanced.skip_tags_regex.value\'\n-#end if\n-#if \'$advanced.random_seed\' != 0:\n- --random-seed=\'$advanced.random_seed\'\n-#end if\n- -S \'$out_counts\'\n-\n-\n-#if str($cond_extra.prepender) != "none":\n-#set $replacer = re.sub(\'[^\\w\\_]+\', \'_\', str($input_bam.element_identifier.rsplit(\'.\',1)[0]))\n- #if str($cond_extra.prepender) == "string":\n-#set $replacer = str($cond_extra.custom_label)\n- #end if\n-\n-&& sed -i -r \'1s|\\b([ACGT]+)\\b|\'"$replacer"\'_\\1|g\' \'$out_counts\'\n-#end if\n-\n+ umi_tools count\n+ \'$wide_format_cell_counts\'\n+ @BARCODE_OPTIONS@\n+ @UMI_GROUPING_OPTIONS@\n+ @SC_OPTIONS@\n+ @SAMBAM_OPTIONS@\n+ @ADVANCED_OPTIONS@\n+ -I \'$input_file\' -S \'$out_counts\'\n+ @LOG@\n+ #if str($cond_extra.prepender) != "none":\n+ #if str($cond_extra.prepender) == "string":\n+ #set $replacer = str($cond_extra.custom_label)\n+ #else\n+ #set $replacer = re.sub(\'[^\\w\\_]+\', \'_\', str($input.element_identifier.rsplit(\'.\',1)[0]))\n+ #end if\n+ && sed -i -r \'1s|\\b([ACGT]+)\\b|\'"$replacer"\'_\\1|g\' \'$out_counts\'\n+ #end if\n ]]></command>\n <inputs>\n- <param name="input_bam" type="data" format="bam" label="Sorted BAM file" help="Please use the samtools sort tool to ensure a correct BAM input" />\n- <param argument="--paired" type="boolean" truevalue="--paired" falsevalue="" checked="false" label="Bam is paired-end" help="both read pairs will be output. This will also force the use of the template length to determine reads with the same mapping coordinates." />\n- <conditional name="barcodes" >\n- <param argument="--extract-umi-method" name="extract_umi_method" type="select" label="Umi Extract Method" help="How are the barcodes encoded in the read?" >\n- <option value="read_id" selected="true">Barcodes are contained at the end of the read seperated by a delimiter</option>\n- <option value="tag" >Barcodes are contained in tags</option>\n- <option value="umis" >Barcodes were extracted using umis</option>\n- </param>\n- '..b'ts" />\n </test>\n <test><!-- count ENSDARG00000019692, relabel string -->\n- <param name="input_bam" value="fc.ENSDARG00000019692.bam" />\n- <param name="method" value="unique" />\n+ <param name="input" value="fc.ENSDARG00000019692.bam" />\n+ <section name="advanced">\n+ <param name="random_seed" value="0" />\n+ </section>\n+ <section name="sc">\n+ <param name="gene_tag" value="XT" />\n+ <param name="per_cell" value="true" />\n+ </section>\n+ <section name="umi">\n+ <param name="method" value="unique" />\n+ </section>\n <conditional name="cond_extra" >\n <param name="prepender" value="string" />\n <param name="custom_label" value="test" />\n@@ -183,8 +175,17 @@\n <output name="out_counts" value="fc.ENSDARG00000019692.counts.test" />\n </test>\n <test><!-- count ENSDARG00000019692, relabel filename -->\n- <param name="input_bam" value="fc.ENSDARG00000019692.bam" />\n- <param name="method" value="unique" />\n+ <param name="input" value="fc.ENSDARG00000019692.bam" />\n+ <section name="advanced">\n+ <param name="random_seed" value="0" />\n+ </section>\n+ <section name="sc">\n+ <param name="gene_tag" value="XT" />\n+ <param name="per_cell" value="true" />\n+ </section>\n+ <section name="umi">\n+ <param name="method" value="unique" />\n+ </section>\n <conditional name="cond_extra" >\n <param name="prepender" value="dataset name" />\n </conditional>\n@@ -193,26 +194,36 @@\n </tests>\n <help><![CDATA[\n \n-UMI Tools count - Count reads per gene from BAM using UMIs\n-----------------------------------------------------------\n+count - Count reads per gene from BAM using UMIs and mapping coordinates\n+========================================================================\n \n-Purpose\n--------\n-\n-The purpose of this command is to count the number of reads per gene based\n-on the mapping co-ordinate and the UMI attached to the read.\n-\n+This tool is only designed to work with library preparation\n+methods where the fragmentation occurs after amplification, as per\n+most single cell RNA-Seq methods (e.g 10x, inDrop, Drop-seq, SCRB-seq\n+and CEL-seq2). Since the precise mapping co-ordinate is not longer\n+informative for such library preparations, it is simplified to the\n+gene. This is a reasonable approach providing the number of available\n+UMIs is sufficiently high and the sequencing depth is sufficiently low\n+that the probability of two reads from the same gene having the same\n+UMIs is acceptably low.\n \n-It is assumed that the FASTQ files were processed with extract_umi.py\n-before mapping and thus the UMI is the last word of the read name. e.g:\n-\n-@HISEQ:87:00000000_AATT\n+If you want to count reads per gene for library preparations which\n+fragment prior to amplification (e.g bulk RNA-Seq), please use\n+``umi_tools dedup`` to remove the duplicate reads as this will use the\n+full information from the mapping co-ordinate. Then use a read\n+counting tool such as FeatureCounts or HTSeq to count the reads per\n+gene.\n \n-where AATT is the UMI sequeuence.\n+In the rare case of bulk RNA-Seq using a library preparation method\n+with fragmentation after amplification, one can still use ``count`` but\n+note that it has not been tested on bulk RNA-Seq.\n \n-If you have used an alternative method which does not separate the\n-read id and UMI with a "_", such as bcl2fastq which uses ":", you can\n-specify the separator, or if your UMIs are encoded in a tag you can also specify this.\n+This tool deviates from group and dedup in that the ``--per-gene`` option\n+is hardcoded on.\n+\n+@BARCODE_HELP@\n+\n+@UMI_GROUPING_HELP@\n \n ]]></help>\n <expand macro="citations" />\n' |