# HG changeset patch
# User cjav
# Date 1379629677 14400
# Node ID 84df983ce1a8b44ca46857e9e66cfb1c86a7c559
First tool_shed release. Using ngs-tools version 0.1.6.
diff -r 000000000000 -r 84df983ce1a8 ngs-tools_split_by_barcode.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ngs-tools_split_by_barcode.xml Thu Sep 19 18:27:57 2013 -0400
@@ -0,0 +1,84 @@
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+ ngs-tools
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+ ngs-tools split-by-barcode
+ $trim_barcode $input_format.format
+ --barcode-size $barcode_length --max-distance $max_distance
+ #if $barcodes
+ --barcodes $barcodes
+ #end if
+ --report $output1 --galaxy $output1.id --output $__new_file_path__
+ $barcode_index
+ #for $i in $input_format.inputs
+ ${i.input}
+ #end for
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+**What it does**
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+This tool splits FASTQ or FASTA datasets into several datasets, using barcodes as the split criteria.
+
+--------
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+**Barcode index format**
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+Barcode index datasets are simple tab separated files.
+Each line should contain an identifier (descriptive name for the barcode), and the barcode itself (A/C/G/T), separated by a TAB character.
+Example::
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+ RL001 ACACGACGACT
+ RL002 ACACGTAGTAT
+ RL003 ACACTACTCGT
+ RL004 ACGACACGTAT
+ RL005 ACGAGTAGACT
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+For each barcode, a new FASTQ or FASTA dataset will be created (with the barcode's identifier as part of the dataset name).
+Sequences matching the barcode will be stored in the appropriate dataset.
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+One additional FASTQ or FASTA dataset will be created (the 'Unassigned' dataset), where sequences not matching any barcode will be stored.
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+The output of this tool is one history dataset per each barcode provided plus a report with the split counts.
+
+------
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+This tool is based on `ngs-tools`__ by Carlos Borroto <carlos.borroto@gmail.com>.
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+ .. __: https://github.com/cjav/ngs-tools/
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diff -r 000000000000 -r 84df983ce1a8 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Thu Sep 19 18:27:57 2013 -0400
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