Mercurial > repos > iuc > umi_tools_extract
changeset 11:a472e995d157 draft
"planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"
| author | iuc |
|---|---|
| date | Tue, 27 Aug 2019 17:10:51 -0400 |
| parents | 828dba98cdb4 |
| children | d5ff68d2d5ff |
| files | macros.xml test-data/out_wl_single.txt test-data/out_wl_user.single.html test-data/out_wl_user.single.tresh.tab test-data/out_wl_user.single.txt test-data/testYYY.40k.fastq.gz umi-tools_extract.xml |
| diffstat | 7 files changed, 119 insertions(+), 42 deletions(-) [+] |
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--- 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 @@ <?xml version="1.0"?> <macros> + <macro name="barcode_sanitizer" > + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value="(" /><!-- left bracket --> + <add value=")" /><!-- right bracket --> + <add value="*" /><!-- asterisk --> + <add value="," /><!-- comma --> + <add value="." /><!-- period --> + <add value="<" /><!-- less than --> + <add value="=" /><!-- equals sign --> + <add value=">" /><!-- greater than --> + <add value="?" /><!-- question mark --> + <add value="_" /><!-- underscore --> + <add value="{"/><!-- left brace --> + <add value="}"/><!-- right brace --> + </valid> + </sanitizer> + </macro> <macro name="barcode2_conditional" > <conditional name="barcode"> <param name="barcode_select" argument="--split-barcode" type="select" label="Barcode on both reads?"> @@ -11,6 +29,7 @@ <param name="bc_pattern2" argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read" help="Use this option to specify the format of the UMI/barcode for the second read pair if required." > + <expand macro="barcode_sanitizer" /> </param> </when> </conditional> @@ -55,7 +74,7 @@ <yield /> </requirements> </xml> - <token name="@VERSION@">0.5.3</token> + <token name="@VERSION@">0.5.5</token> <token name="@COMMAND_LINK@"><![CDATA[ #set $gz = False #if $input_type.type == 'single':
--- a/test-data/out_wl_single.txt Fri Aug 17 09:41:59 2018 -0400 +++ b/test-data/out_wl_single.txt Tue Aug 27 17:10:51 2019 -0400 @@ -1,44 +1,4 @@ -# output generated by whitelist --bc-pattern=CCCCCCCCNNNNNNNN --subset-reads=0 --stdin=/tmp/tmpibtvD6/files/000/dataset_1.dat --method=reads --plot-prefix=OUT --3prime -# job started at Sun Feb 25 10:49:56 2018 on bag -- cb0db520-8a4e-4040-aa88-93efc0718fa8 -# pid: 2217, system: Linux 4.13.0-32-generic #35-Ubuntu SMP Thu Jan 25 09:13:46 UTC 2018 x86_64 -# blacklist_tsv : None -# cell_number : False -# compresslevel : 6 -# error_correct_threshold : 1 -# expect_cells : False -# extract_method : string -# filter_cell_barcodes : False -# log2stderr : False -# loglevel : 1 -# method : reads -# pattern : CCCCCCCCNNNNNNNN -# pattern2 : None -# plot_prefix : OUT -# prime3 : True -# random_seed : None -# read2_in : None -# short_help : None -# stderr : <_io.TextIOWrapper name='<stderr>' 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='<stdout>' mode='w' 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 -# 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
--- /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 @@ +<html> <head></head><body> <h1>Cell and Count Metrics</h1> <img src="OUT_cell_barcode_count_density.png" ><br /> <img src="OUT_cell_barcode_knee.png" ><br /> <img src="OUT_cell_barcode_counts.png" ><br /> </body></html>
--- /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
--- /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
--- 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 @@ -<tool id="umi_tools_extract" name="UMI-tools extract" version="@VERSION@.2"> +<tool id="umi_tools_extract" name="UMI-tools extract" version="@VERSION@.0"> <description>Extract UMI from fastq files</description> <macros> <import>macros.xml</import>