# HG changeset patch
# User jackcurragh
# Date 1649842722 0
# Node ID b4479aea41df22c6ef0e0b5fa701aef20ebc7ee9
# Parent 60b449221e6a0ff486e6987a9c9d4d48f2a59c57
Uploaded
diff -r 60b449221e6a -r b4479aea41df cutadapt.xml
--- a/cutadapt.xml Wed Apr 13 09:15:28 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1371 +0,0 @@
-
- Remove adapter sequences from FASTQ/FASTA
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- macros.xml
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- cutadapt --version
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- report.txt
-#end if
- ]]>
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- library['type'] != 'paired_collection' and 'multiple_output' not in output_selector
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- library['type'] == 'paired' and 'multiple_output' not in output_selector
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- library['type'] == 'paired_collection' and 'multiple_output' not in output_selector
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- output_selector and 'report' in output_selector
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- output_selector and 'info_file' in output_selector
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- output_selector and 'rest_file' in output_selector
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- output_selector and 'wildcard_file' in output_selector
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- output_selector and 'untrimmed_file' in output_selector
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- library['type'] == 'paired' or library['type'] == 'paired_collection'
- output_selector and 'untrimmed_file' in output_selector
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- output_selector and 'too_short_file' in output_selector
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- library['type'] == 'paired' or library['type'] == 'paired_collection'
- output_selector and 'too_short_file' in output_selector
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- output_selector and 'too_long_file' in output_selector
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- library['type'] == 'paired' or library['type'] == 'paired_collection'
- output_selector and 'too_long_file' in output_selector
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- output_selector and 'json_stats' in output_selector
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- output_selector and 'multiple_output' in output_selector
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diff -r 60b449221e6a -r b4479aea41df cutadapt/cutadapt.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cutadapt/cutadapt.xml Wed Apr 13 09:38:42 2022 +0000
@@ -0,0 +1,629 @@
+
+ Remove adapter sequences from FASTQ/FASTA
+
+ macros.xml
+
+
+
+
+ cutadapt --version
+
+ report.txt
+#end if
+ ]]>
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+ [0-9,]+
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+ [A-Za-z0-9 =-_/+]+
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+ [A-Za-z0-9 {}=_]+
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+ library['type'] != 'paired_collection' and 'multiple_output' not in output_selector
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+ library['type'] == 'paired' and 'multiple_output' not in output_selector
+
+
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+ library['type'] == 'paired_collection' and 'multiple_output' not in output_selector
+
+
+
+
+
+ output_selector and 'report' in output_selector
+
+
+ output_selector and 'info_file' in output_selector
+
+
+
+ output_selector and 'rest_file' in output_selector
+
+
+
+
+ output_selector and 'wildcard_file' in output_selector
+
+
+
+ output_selector and 'untrimmed_file' in output_selector
+
+
+
+ library['type'] == 'paired' or library['type'] == 'paired_collection'
+ output_selector and 'untrimmed_file' in output_selector
+
+
+
+
+ output_selector and 'too_short_file' in output_selector
+
+
+
+ library['type'] == 'paired' or library['type'] == 'paired_collection'
+ output_selector and 'too_short_file' in output_selector
+
+
+
+ output_selector and 'too_long_file' in output_selector
+
+
+
+ library['type'] == 'paired' or library['type'] == 'paired_collection'
+ output_selector and 'too_long_file' in output_selector
+
+
+
+ output_selector and 'json_stats' in output_selector
+
+
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+ output_selector and 'multiple_output' in output_selector
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+ ]]>
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diff -r 60b449221e6a -r b4479aea41df cutadapt/macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cutadapt/macros.xml Wed Apr 13 09:38:42 2022 +0000
@@ -0,0 +1,393 @@
+
+ 3.7
+ 0
+ fastq.gz,fastq,fasta
+
+
+ topic_0632
+
+
+ operation_0231
+
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+
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+ cutadapt
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+ 10.14806/ej.17.1.200
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+ cutadapt
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diff -r 60b449221e6a -r b4479aea41df cutadapt/static/images/adapters.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cutadapt/static/images/adapters.svg Wed Apr 13 09:38:42 2022 +0000
@@ -0,0 +1,259 @@
+
+
+
+
diff -r 60b449221e6a -r b4479aea41df cutadapt/test-data/bwa-mem-fastq1.fq.gz
Binary file cutadapt/test-data/bwa-mem-fastq1.fq.gz has changed
diff -r 60b449221e6a -r b4479aea41df cutadapt/test-data/cutadapt_out1.fq.gz
Binary file cutadapt/test-data/cutadapt_out1.fq.gz has changed
diff -r 60b449221e6a -r b4479aea41df cutadapt/test-data/cutadapt_small.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cutadapt/test-data/cutadapt_small.fastq Wed Apr 13 09:38:42 2022 +0000
@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+CGTCCGAANTAGCTACCACCCTGATTAGACAAAT
++
+)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5
+@prefix:1_13_1259/1
+AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT
++
+;<:&:A;A!9<<<,7:<=3=;:<&8<;=<&
+@prefix:1_13_1440/1
+CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC
++
+<=A:A=57!7<';<6?5;;6:+:=)71>70<,=:
diff -r 60b449221e6a -r b4479aea41df cutadapt/test-data/cutadapt_small.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cutadapt/test-data/cutadapt_small.out Wed Apr 13 09:38:42 2022 +0000
@@ -0,0 +1,12 @@
+@prefix:1_13_573/1
+CGTCCGAANTAGCTACCACCCTGATTAGACAAAT
++
+)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5
+@prefix:1_13_1259/1
+AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT
++
+;<:&:A;A!9<<<,7:<=3=;:<&8<;=<&
+@prefix:1_13_1440/1
+CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC
++
+<=A:A=57!7<';<6?5;;6:+:=)71>70<,=:
diff -r 60b449221e6a -r b4479aea41df cutadapt/tool-data/adapters.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cutadapt/tool-data/adapters.loc.sample Wed Apr 13 09:38:42 2022 +0000
@@ -0,0 +1,14 @@
+#
+# Adapter/Linker sequences for FASTX-Clipper tool.
+# Also used by cutadapt tool
+#
+# Format:
+# Adapter Sequence Descriptive name
+#
+# Example:
+# AAATTTGATAAGATA Our-Adapter
+#
+# Some adapters can be found here:
+# http://seqanswers.com/forums/showthread.php?t=198
+
+TGTAGGCC Dummy-Adapter (do not use me)
diff -r 60b449221e6a -r b4479aea41df cutadapt/tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cutadapt/tool_data_table_conf.xml.sample Wed Apr 13 09:38:42 2022 +0000
@@ -0,0 +1,7 @@
+
+
+
+
diff -r 60b449221e6a -r b4479aea41df cutadapt/tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cutadapt/tool_data_table_conf.xml.test Wed Apr 13 09:38:42 2022 +0000
@@ -0,0 +1,6 @@
+
+
+