Repository 'umi_tools_group'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_group

Changeset 9:3b8fecdf9058 (2019-08-27)
Previous changeset 8:aa5ec9b8c99a (2018-07-20) Next changeset 10:a24f5b991320 (2019-09-10)
Commit message:
"planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"
modified:
macros.xml
test-data/out_wl_single.txt
added:
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
b
diff -r aa5ec9b8c99a -r 3b8fecdf9058 macros.xml
--- a/macros.xml Fri Jul 20 03:48:54 2018 -0400
+++ b/macros.xml Tue Aug 27 17:10:29 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="&#40;" /><!-- left bracket -->
+                <add value="&#41;" /><!-- right bracket -->
+                <add value="&#42;" /><!-- asterisk -->
+                <add value="&#44;" /><!-- comma -->
+                <add value="&#46;" /><!-- period -->
+                <add value="&#60;" /><!-- less than -->
+                <add value="&#61;" /><!-- equals sign -->
+                <add value="&#62;" /><!-- greater than -->
+                <add value="&#63;" /><!-- question mark -->
+                <add value="&#95;" /><!-- underscore -->
+                <add value="&#123;"/><!-- left brace -->
+                <add value="&#125;"/><!-- 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':
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diff -r aa5ec9b8c99a -r 3b8fecdf9058 test-data/out_wl_single.txt
--- a/test-data/out_wl_single.txt Fri Jul 20 03:48:54 2018 -0400
+++ b/test-data/out_wl_single.txt Tue Aug 27 17:10:29 2019 -0400
b
@@ -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
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diff -r aa5ec9b8c99a -r 3b8fecdf9058 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 17:10:29 2019 -0400
b
@@ -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>
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diff -r aa5ec9b8c99a -r 3b8fecdf9058 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 17:10:29 2019 -0400
b
@@ -0,0 +1,7 @@
+count action
+2 Rejected
+8 Rejected
+11 Rejected
+27 Rejected
+90 Selected
+404 Rejected
b
diff -r aa5ec9b8c99a -r 3b8fecdf9058 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 17:10:29 2019 -0400
b
@@ -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
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diff -r aa5ec9b8c99a -r 3b8fecdf9058 test-data/testYYY.40k.fastq.gz
b
Binary file test-data/testYYY.40k.fastq.gz has changed