# HG changeset patch
# User greg
# Date 1637541039 0
# Node ID 54380a6171b8b51e43e6d73d74e964ba10049ec0
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/misc/sample_names commit b935f36cfe430263564503ebb71f78dc79315acb"
diff -r 000000000000 -r 54380a6171b8 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Nov 22 00:30:39 2021 +0000
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+ 1.0
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+ 21.01
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+ @misc{None,
+ journal = {None},
+ author = {1. Von Kuster G},
+ title = {Manuscript in preparation},
+ year = {None},
+ url = {https://github.com/USDA-VS/vSNP},}
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diff -r 000000000000 -r 54380a6171b8 sample_names.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/sample_names.xml Mon Nov 22 00:30:39 2021 +0000
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+ from input file names
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+ macros.xml
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+ '$output'
+]]>
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+**What it does**
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+Accepts fastqsanger sample files, extracts a unique portion of the file name as the sample name, and writes it to
+the output. The output text file can be consumed by the **Parse parameter value** expression tool to provide workflow
+parameter values to the **Read group identifier (ID)** and the **Sample name identifier (SM)** parameters in the
+**Map with BWA-MEM** tool.
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diff -r 000000000000 -r 54380a6171b8 test-data/CMC_20E1_R1.fastq.gz
diff -r 000000000000 -r 54380a6171b8 test-data/CMC_20E1_R2.fastq.gz
diff -r 000000000000 -r 54380a6171b8 test-data/SRR14085881_forward
Binary file test-data/SRR14085881_forward has changed
diff -r 000000000000 -r 54380a6171b8 test-data/SRR14085881_reverse
Binary file test-data/SRR14085881_reverse has changed
diff -r 000000000000 -r 54380a6171b8 test-data/sample_names.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_names.txt Mon Nov 22 00:30:39 2021 +0000
@@ -0,0 +1,1 @@
+CMC_20E1_R1_fastq_gz
diff -r 000000000000 -r 54380a6171b8 test-data/sample_names2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_names2.txt Mon Nov 22 00:30:39 2021 +0000
@@ -0,0 +1,1 @@
+CMC_20E1_R
diff -r 000000000000 -r 54380a6171b8 test-data/sample_names3.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_names3.txt Mon Nov 22 00:30:39 2021 +0000
@@ -0,0 +1,1 @@
+CMC_20E1_R
diff -r 000000000000 -r 54380a6171b8 test-data/sample_names4.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_names4.txt Mon Nov 22 00:30:39 2021 +0000
@@ -0,0 +1,1 @@
+SRR14085881_