| Previous changeset 13:49bfe13676a1 (2021-02-10) Next changeset 15:81bebc3027fc (2021-10-23) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79" |
|
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_whitelist.xml |
|
added:
test-data/chr19_gene_tags.sam test-data/group_in2.sam |
| b |
| diff -r 49bfe13676a1 -r 345bdf4546fd macros.xml --- a/macros.xml Wed Feb 10 19:29:21 2021 +0000 +++ b/macros.xml Mon Sep 13 14:50:19 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 49bfe13676a1 -r 345bdf4546fd 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 14:50:19 2021 +0000 |
| b |
| 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' |
| b |
| diff -r 49bfe13676a1 -r 345bdf4546fd test-data/dedup_out1.bam |
| b |
| Binary file test-data/dedup_out1.bam has changed |
| b |
| diff -r 49bfe13676a1 -r 345bdf4546fd test-data/dedup_out2.bam |
| b |
| Binary file test-data/dedup_out2.bam has changed |
| b |
| diff -r 49bfe13676a1 -r 345bdf4546fd test-data/dedup_out3.bam |
| b |
| Binary file test-data/dedup_out3.bam has changed |
| b |
| diff -r 49bfe13676a1 -r 345bdf4546fd test-data/dedup_out4.bam |
| b |
| Binary file test-data/dedup_out4.bam has changed |
| b |
| diff -r 49bfe13676a1 -r 345bdf4546fd test-data/dedup_out5.bam |
| b |
| Binary file test-data/dedup_out5.bam has changed |
| b |
| diff -r 49bfe13676a1 -r 345bdf4546fd test-data/dedup_out6.bam |
| b |
| Binary file test-data/dedup_out6.bam has changed |
| b |
| diff -r 49bfe13676a1 -r 345bdf4546fd test-data/group_in2.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/group_in2.sam Mon Sep 13 14:50:19 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 49bfe13676a1 -r 345bdf4546fd test-data/group_out4.bam |
| b |
| Binary file test-data/group_out4.bam has changed |
| b |
| diff -r 49bfe13676a1 -r 345bdf4546fd test-data/group_out4.tab --- a/test-data/group_out4.tab Wed Feb 10 19:29:21 2021 +0000 +++ b/test-data/group_out4.tab Mon Sep 13 14:50:19 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 49bfe13676a1 -r 345bdf4546fd test-data/out_wl_paired.log --- a/test-data/out_wl_paired.log Wed Feb 10 19:29:21 2021 +0000 +++ b/test-data/out_wl_paired.log Mon Sep 13 14:50:19 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 49bfe13676a1 -r 345bdf4546fd umi-tools_whitelist.xml --- a/umi-tools_whitelist.xml Wed Feb 10 19:29:21 2021 +0000 +++ b/umi-tools_whitelist.xml Mon Sep 13 14:50:19 2021 +0000 |
| [ |
| b'@@ -1,17 +1,24 @@\n-<tool id="umi_tools_whitelist" name="UMI-tools whitelist" version="@VERSION@.0">\n+<tool id="umi_tools_whitelist" name="UMI-tools whitelist" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n <description>Extract cell barcodes from FASTQ files</description>\n+ <expand macro="bio_tools"/>\n <macros>\n <import>macros.xml</import>\n </macros>\n <expand macro="requirements" />\n <command detect_errors="exit_code"><![CDATA[\n+ #import json\n @COMMAND_LINK@\n-\n umi_tools whitelist\n- --bc-pattern=\'$bc_pattern\'\n- --extract-method=\'$extract_method\'\n+ \n+ @FASTQ_BARCODE_EXTRACTION_OPTIONS@ \n+\n --subset-reads=\'$subset_reads\'\n- #if $input_type.type == \'single\':\n+ $allow_threshold_error\n+ #if $ed_above_threshold\n+ --ed-above-threshold=$ed_above_threshold\n+ #end if\n+ --knee-method=\'$knee_method\'\n+ #if $input_type_cond.input_type == \'single\':\n #if $gz:\n --stdin=input_single.gz\n #else\n@@ -25,30 +32,20 @@\n --stdin=input_read1.txt\n --read2-in=input_read2.txt\n #end if\n- #if $input_type.barcode.barcode_select == "both_reads":\n- --bc-pattern2=\'$input_type.barcode.bc_pattern2\'\n- #end if\n #end if\n #if $celloptions.use_cell_opts == "advanced":\n- #if $celloptions.set_cell_number != "0":\n+ #if str($celloptions.set_cell_number) != \'\':\n --set-cell-number=$celloptions.set_cell_number\n #end if\n- #if $celloptions.expect_cells != "0":\n+ #if str($celloptions.expect_cells) != \'\':\n --expect-cells=$celloptions.expect_cells\n #end if\n- --error-correct-threshold=$celloptions.error_correct_thresh\n+ --error-correct-threshold=$celloptions.error_correct_threshold\n #end if\n --method=$method\n --plot-prefix=OUT\n \n- $prime3\n-\n- #if $log:\n- --log=\'$out_log\'\n- #end if\n-\n- --log2stderr\n-\n+ @LOG@\n > \'$out_whitelist\' &&\n \n mkdir \'${ out_html_report.files_path }\' &&\n@@ -66,28 +63,24 @@\n ]]></command>\n <inputs>\n <expand macro="input_types" />\n- <param name="bc_pattern" 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- <expand macro="barcode_sanitizer" />\n- </param>\n- <param name="extract_method" argument="--extract-method" type="select" label="Barcode Extraction Method"\n- help="If bracketed expressions are used in the above barcode pattern, then set this to \'regex\'. Otherwise leave as \'string\'" >\n- <option value="string" selected="true" />\n- <option value="regex" />\n- </param>\n- <param name="method" argument="--method" type="select" label="Count reads or UMIs"\n- help="Many published protocols rank CBs by the number of reads the CBs appear in. However you could also use the number of unique UMIs a CB is associated with. Note that this is still and approximation to the number of transcripts captured because the same UMI could be associated with two different transcripts and be counted as independent." >\n+ <expand macro="fastq_barcode_extraction_options_macro"/>\n+\n+ <param argument="--method" type="select" label="Cou'..b' >\n- <param name="type" value="single" />\n- <param name="input_single" value="testYYY.40k.fastq.gz" ftype="fastq.gz" />\n+ <test expect_num_outputs="4">\n+ <conditional name="input_type_cond" >\n+ <param name="input_type" value="single" />\n+ <param name="input_read1" value="testYYY.40k.fastq.gz" ftype="fastqsanger.gz" />\n </conditional>\n <param name="bc_pattern" value="(?P<cell_1>.{8,10})(?P<discard_1>ACTGGCCTGCGA){s<=3}(?P<cell_2>.{9})(?P<discard_2>GGTAGCGGTGACA){s<=3}(?P<cell_3>.{9})(?P<umi_1>.{8})T{3}.*" />\n <param name="extract_method" value="regex" />\n <param name="method" value="umis" />\n+ <param name="knee_method" value="density"/>\n <param name="prime3" value="true" />\n+ <param name="filtered_out_bool" value="true"/>\n <output name="out_whitelist" file="out_wl_user.single.txt" />\n <output name="out_thresh" file="out_wl_user.single.tresh.tab" />\n <output name="out_html_report" file="out_wl_user.single.html" />\n+ <output name="filtered_out">\n+ <assert_contents>\n+ <has_text text="@A00250:74:HFMFVDSXX:2:1101:1027:1016 1:N:0:GTAGAGGA"/>\n+ </assert_contents>\n+ </output>\n </test>\n </tests>\n <help><![CDATA[\n@@ -195,75 +212,8 @@\n Extract cell barcodes and identify the most likely true barcodes using\n the \'knee\' method.\n \n-Options\n--------\n-\n---bc-pattern\n- This should be used where the barcodes are always in the same\n- place in the read.\n-\n- - N = UMI position (required)\n- - C = cell barcode position (optional)\n- - X = sample position (optional)\n-\n- Bases with Ns and Cs will be extracted and added to the read\n- name. The corresponding sequence qualities will be removed from\n- the read. Bases with an X will be reattached to the read.\n-\n- E.g. If the pattern is NNNNCC,\n- Then the read:\n- @HISEQ:87:00000000 read1\n- AAGGTTGCTGATTGGATGGGCTAG\n- DA1AEBFGGCG01DFH00B1FF0B\n- +\n- will become:\n- @HISEQ:87:00000000_TT_AAGG read1\n- GCTGATTGGATGGGCTAG\n- 1AFGGCG01DFH00B1FF0B\n- +\n-\n- where \'TT\' is the cell barcode and \'AAGG\' is the UMI.\n-\n+@FASTQ_BARCODE_EXTRACTION_HELP@\n \n---set-cell-number\n- Use this option to explicity set the number of cell barcodes\n- which should be accepted. Note that the exact number of cell\n- barcodes in the outputted whitelist may be slightly less than\n- this if there are multiple cells observed with the same\n- frequency at the threshold between accepted and rejected cell\n- barcodes.\n-\n---expect-cells=[EXPECTED_CELLS]\n- An upper limit estimate for the number of inputted cells. The knee\n- method will now select the first threshold (order ascendingly)\n- which results in the number of cell barcodes accepted being <=\n- EXPECTED_CELLS and > EXPECTED_CELLS * 0.1.\n-\n-\n---bc-pattern2\n- Use this option to specify the format of the UMI/barcode for\n- the second read pair if required. If --bc-pattern2 is not\n- supplied, this defaults to the same pattern as --bc-pattern\n-\n---3prime\n- By default the barcode is assumed to be on the 5\' end of the read, but\n- use this option to sepecify that it is on the 3\' end instead\n-\n-Usage:\n-------\n-\n-For single ended reads:\n- umi_tools whitelist --bc-pattern=[PATTERN] -L extract.log\n- [OPTIONS]\n-\n-reads from stdin and outputs to stdout.\n-\n-For paired end reads where the cell barcodes is split across the read pairs:\n- umi_tools whitelist --bc-pattern=[PATTERN]\n- --bc-pattern2=[PATTERN] --read2-in=[FASTQIN] -L extract.log\n- [OPTIONS]\n-\n-reads end one from stdin and end two from FASTQIN and outputs to stdin\n \n \n Output:\n' |