# HG changeset patch # User iuc # Date 1566940251 14400 # Node ID a472e995d1571290d8792a827a447d15ff7e8632 # Parent 828dba98cdb43ff820b68adf7089f66d227b4b58 "planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0" diff -r 828dba98cdb4 -r a472e995d157 macros.xml --- a/macros.xml Fri Aug 17 09:41:59 2018 -0400 +++ b/macros.xml Tue Aug 27 17:10:51 2019 -0400 @@ -1,5 +1,23 @@ + + + + + + + + + + + + + + + + + + @@ -11,6 +29,7 @@ + @@ -55,7 +74,7 @@ - 0.5.3 + 0.5.5 ' mode='w' encoding='UTF-8'> -# stdin : <_io.TextIOWrapper name='/tmp/tmpibtvD6/files/000/dataset_1.dat' mode='r' encoding='UTF-8'> -# stdlog : <_io.TextIOWrapper name='' mode='w' encoding='UTF-8'> -# stdout : <_io.TextIOWrapper name='' mode='w' encoding='UTF-8'> -# subset_reads : 0 -# timeit_file : None -# timeit_header : None -# timeit_name : all -# whitelist_tsv : None -## 2018-02-25 10:49:56,061 INFO Starting barcode extraction -## 2018-02-25 10:49:56,061 INFO Parsed 0 reads -## 2018-02-25 10:49:56,062 INFO Starting - whitelist determination -## 2018-02-25 10:49:57,383 INFO Finished - whitelist determination -## 2018-02-25 10:49:57,383 INFO Starting - finding putative error cell barcodes -## 2018-02-25 10:49:57,383 INFO Finished - finding putative error cell barcodes -## 2018-02-25 10:49:57,383 INFO Writing out whitelist AAAAAAAA AAAAAACA,AAACAAAA,AATAAAAA 3 1,1,1 ACAAAAAC 2 ACAACAAA 2 TTACTTAA TTACTAAA 2 1 -## 2018-02-25 10:49:57,383 INFO Parsed 100 reads -## 2018-02-25 10:49:57,383 INFO 100 reads matched the barcode pattern -## 2018-02-25 10:49:57,383 INFO Found 95 unique cell barcodes -# job finished in 1 seconds at Sun Feb 25 10:49:57 2018 -- 2.25 0.06 0.00 0.00 -- cb0db520-8a4e-4040-aa88-93efc0718fa8 diff -r 828dba98cdb4 -r a472e995d157 test-data/out_wl_user.single.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_wl_user.single.html Tue Aug 27 17:10:51 2019 -0400 @@ -0,0 +1,1 @@ +

Cell and Count Metrics




diff -r 828dba98cdb4 -r a472e995d157 test-data/out_wl_user.single.tresh.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_wl_user.single.tresh.tab Tue Aug 27 17:10:51 2019 -0400 @@ -0,0 +1,7 @@ +count action +2 Rejected +8 Rejected +11 Rejected +27 Rejected +90 Selected +404 Rejected diff -r 828dba98cdb4 -r a472e995d157 test-data/out_wl_user.single.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_wl_user.single.txt Tue Aug 27 17:10:51 2019 -0400 @@ -0,0 +1,90 @@ +AACCGCCTCAGGCAGCTATCTCGGTTA 6 +AACCGCCTCCTCTCTCAAACTACATAT TACCGCCTCCTCTCTCAAACTACATAT 4 1 +AAGACATGCAGTGAAAGGACAAACTTT 3 +ACACGCCGGTTCCATTGAGCAACATTA 3 +ACCAAGGACACTGTTAGAAAGTTTACG ACCAAGGACACTGTAAGAAAGTTTACG 3 1 +ACCCTGACCACAGTGGTACTACATGCG 4 +ACGAAAGGTCGTTCGGTATACTTCGGA TCGAAAGGTCGTTCGGTATACTTCGGA 3 1 +AGAGCTATGAAGAGTAGAAAGCCTTCT 3 +AGCCATCACAGCGACACCTCTCACGGA TGCCATCACAGCGACACCTCTCACGGA 6 1 +ATCAGAGCTAACCCTCGGAAGGGTCAG TTCAGAGCTAACCCTCGGAAGGGTCAG 3 1 +ATCCCGGAGGTACATCTACATAGGTCA 3 +ATGTAATGGTAGTCTTGAACGCTGTTG 3 +CAAACCGCCACGACCACCAAGTTTACG 3 +CAAACCGCCTGACAGACAAATGTATCG CAAACCGTCTGACAGACAAATGTATCG,GAAACCGCCTGACAGACAAATGTATCG 3 1,1 +CAAAGGCACAACCAAAGTACTAGACCG 3 +CAAAGGCACAACCCTCGGACTCATACG CAAAGGCACGACCCTCGGACTCATACG,GAAAGGCACAACCCTCGGACTCATACG 3 1,1 +CAAAGGCACAATCAGTTTATGGGACTC 3 +CAAAGGCACGATGAACTGGCTCCTTGA GAAAGGCACGATGAACTGGCTCCTTGA 4 1 +CAAAGGCACTAGGGATACCATAGGTCA GAAAGGCACTAGGGATACCATAGGTCA 4 1 +CAAGCAAGCGATGAACTGCAATACAAG 3 +CACACACTACACCCAAAGGTAGAAGCA GACACACTACACCCAAAGGTAGAAGCA 4 1 +CACATTGCAAAACGTACCAAGGCCGCA 3 +CAGCAAGATTTGGAGGTAAGTCTGTAC 3 +CAGCTGACATACAGGATATCCGTCTTA 3 +CCACTTGGAAAACTGCGCAAATGGAGG 3 +CTATGAAATCTCTCTCAAAAATTACAG GTATGAAATCTCTCTCAAAAATTACAG 4 1 +CTTCACATAGTACATCTAGATCAGCGA 3 +GAATCTGTAAAGGACTATAAAGTCATT 4 +GACGGATTAAGTGTTGTCACTCATACG 3 +GACGGATTATATAGCCCTCAATAGGGT 3 +GAGAATCGTCAAGACCTACAGCCTGGC CAGAATCGTCAAGACCTACAGCCTGGC,GGGAATCGTCAAGACCTACAGCCTGGC 3 1,1 +GAGGTGCTAGCCAATGTAGATAGAGGA 3 +GAGTACATTACCAAAATGTGAAGCCAA 3 +GAGTACATTTTGGAGGTAACAACTAGT 3 +GCAATCCGAAGATAGTTCCAGCCTGGC GCAATCCGAAGATAGTACCAGCCTGGC 4 1 +GCAATCCGAAGGCAGCTAAATTCGGCG GCAATCCGAAGGCAGCTGAATTCGGCG 3 1 +GCAATCCGAGAGTGCGAATCCTCAATA GCAATCCGAGAGAGCGAATCCTCAATA,GCAATCCGAGAGTGCGTATCCTCAATA 5 1,1 +GCAATCCGAGCCAATGTAGATGGTCCA 3 +GCACTGTCAGATGAACTGCAAGTAGAA 3 +GCACTGTCAGTGTGTCGACGTCTAGGT 3 +GCCTTACAAGTGCAGTAACTCAAGACA 3 +GCGATTACAAAGCTACTTACTTACGAT GCGATTACAAAGCTACTTCCTTACGAT 4 1 +GCGATTACAATCAACCGAGGCACAACA 3 +GCGATTACATGTTCTCCACAATAGGGT 3 +GCTGCCAATAGGAGGCGCTGAAGCCAA 3 +GCTGCCAATATTCATCGTAGTTGTTCT GCTGCCAATATTCATCGTAGTTGTTCC 7 1 +GCTGCCAATCAACAACGGTGAAGCCAA GCTGCCAATCATCAACGGTGAAGCCAA 6 1 +GCTGCCAATCACCTACCCAAGCCTTCT GATGCCAATCACCTACCCAAGCCTTCT 3 1 +GGATTAGGAAGCTGCCGTGGCACAACA GGAGTAGGAAGCTGCCGTGGCACAACA 3 1 +GGCAAGCAAACCAAAATGACTTACGAT 4 +GGCAAGCAAGATGAACTGCTAAGCTTC 4 +GGCAAGCAATAGTGACTACTACATGCG 3 +GTACAGAACAATCCTGAACTATTAGCC CTACAGAACAATCCTGAACTATTAGCC 3 1 +GTATGAAATATCCAACCGCTGTACGGA 3 +TAAGCGTTACACAAAGGCCACAAGTAT 5 +TAAGCGTTATATAGCCCTCAACCTCCA 4 +TACCGAGCAATCCTAGGATCTCACGGA 3 +TACCGAGCACAAGACCTACGTACTACG 5 +TACCGAGCAGTGTGTCGATCTCACGGA 3 +TACCGCCTCAGGCAGCTATCTCGGTTA TACCGCCTCAGGCAGCTATCTCGGTCA 3 1 +TAGGCGATCAAGCTACTTCGTACTACG AAGGCGATCAAGCTACTTCGTACTACG 3 1 +TAGGCGATCGCTAACTCAACAACTAGT AAGGCGATCGCTAACTCAACAACTAGT 3 1 +TATATTGGGCCGACAAGAAAGGGTCAG AATATTGGGCCGACAAGAAAGGGTCAG,TCTATTGGGCCGACAAGAAAGGGTCAG 3 1,1 +TATCGAATGAAGAGTAGACAGGCATTT AATCGAATGAAGAGTAGACAGGCATTT 3 1 +TCACACAAAAAATAAATATGTATGCGA ACACACAAAAAATAAATATGTATGCGA,TCGCACAAAAAATAAATATGTATGCGA 3 2,1 +TCACGAGATACTTCGAGCAAGCCTTCT ACACGAGATACTTCGAGCAAGCCTTCT,CCACGAGATACTTCGAGCAAGCCTTCT 3 2,1 +TCACGAGATCAACAACGGCGTACTACG ACACGAGATCAACAACGGCGTACTACG 3 1 +TCAGGAGGAACTTGATGACAAGTAGAA 4 +TCAGGAGGACACTTATGTCTAAGCTTC TCAGGAGGACACTTATGTCTACGCTTC,TCAGGAGGACACTTATGTCTCAGCTTC,TNAGGAGGACACTTATGTCTAAGCTTC 6 1,1,1 +TCAGGAGGACTTGCTTCAATCGAGTCT TCAGGAGGACTTGCTTCCATCGAGTCT 3 1 +TCATAAGCGATCCTAGGATTCAGCTCA ACATAAGCGATCCTAGGATTCAGCTCA 3 1 +TCATAAGCGGACACTTAAAGCCGCAAG ACATAAGCGGACACTTAAAGCCGCAAG,TCATAAGCGGACACTTAAAGCCGCGAG,TTATAAGCGGACACTTAAAGCCGCAAG 3 1,1,1 +TCGAAAGGTATTACCAAGGCAACATTA ACGAAAGGTATTACCAAGGCAACATTA 4 1 +TGAACTTCCACAATATGGCAAGTTTCC AGAACTTCCACAATATGGCAAGTTTCC 7 2 +TGAACTTCCATGAGTTACCGTACTACG AGAACTTCCATGAGTTACCGTACTACG,TGAACTTCCATGAGTTACCTTACTACG 6 2,1 +TGAAGCACTCACTCGAGAACACCTTAG 4 +TGAAGCACTGCCAATGTAGAACGACAA AGAAGCACTGCCAATGTAGAACGACAA 3 2 +TGAGCTATGAAGAGTAGAAAGCCTTCT 3 +TGCGATCTACCGTATCTAACAAACTTT 4 +TGGAGATTAATTAGGCATACAGTAAAC 6 +TGGCTCAGAAAGCTACTTGCTCCTTGA TGACTCAGAAAGCTACTTGCTCCTTGA 3 1 +TGGCTCAGAAGAATGGAGAATTCGGCG TGGTTCAGAAGAATGGAGAATTCGGCG 3 1 +TGGCTCAGATGACAGACAAAGGGAACT TGGCTCAGATGACAGACAAAGGGACCT 3 1 +TGTACCTTAGCCAATGTAAAGGGTCAG 3 +TTACTTAGGATGAGTTACTCCGTCTTA ATACTTAGGATGAGTTACTCCGTCTTA 3 1 +TTGTTCCAAAGGTTCGCTACTCATACG 3 +TTTATTACCCCATGCACACATAGGTCA ATTATTACCCCATGCACACATAGGTCA 3 2 +TTTATTACCGTGCAGTAAACTCATACG ATTATTACCGTGCAGTAAACTCATACG 3 1 +TTTGGCTAAACTATCCTCACTACATAT ATTGGCTAAACTATCCTCACTACATAT 3 2 +TTTTAGATGGATGAACTGCAACGATCT ATTTAGATGGATGAACTGCAACGATCT 3 1 diff -r 828dba98cdb4 -r a472e995d157 test-data/testYYY.40k.fastq.gz Binary file test-data/testYYY.40k.fastq.gz has changed diff -r 828dba98cdb4 -r a472e995d157 umi-tools_extract.xml --- a/umi-tools_extract.xml Fri Aug 17 09:41:59 2018 -0400 +++ b/umi-tools_extract.xml Tue Aug 27 17:10:51 2019 -0400 @@ -1,4 +1,4 @@ - + Extract UMI from fastq files macros.xml