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comparison ngs-tools_split_by_barcode.xml @ 2:ee8699b10e83 draft default tip

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Updated to use ngs-tools 0.1.8 with better exception handling and proper writing of error messages to sdterr.
author cjav
date Tue, 15 Oct 2013 13:08:50 -0400
parents 84df983ce1a8
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1:b423473c0131 2:ee8699b10e83
1 <tool id="ngs-tools_split_by_barcode" name="Barcode Splitter (ngs-tools)" force_history_refresh="True" version="1.0.1"> 1 <tool id="ngs-tools_split_by_barcode" name="Barcode Splitter (ngs-tools)" force_history_refresh="True" version="1.0.1">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.1.6">ngs-tools</requirement> 4 <requirement type="package" version="0.1.8">ngs-tools</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command>
7 ngs-tools split-by-barcode 7 ngs-tools split-by-barcode
8 $trim_barcode $input_format.format 8 $trim_barcode $input_format.format
9 --barcode-size $barcode_length --max-distance $max_distance 9 --barcode-size $barcode_length --max-distance $max_distance
35 </when> 35 </when>
36 </conditional> 36 </conditional>
37 <param format="tabular" name="barcode_index" type="data" label="Barcodes index" help="See below for description." /> 37 <param format="tabular" name="barcode_index" type="data" label="Barcodes index" help="See below for description." />
38 <param name="barcode_length" type="integer" size="3" value="11" label="Barcode length" help="Please specify the barcode length." /> 38 <param name="barcode_length" type="integer" size="3" value="11" label="Barcode length" help="Please specify the barcode length." />
39 <param name="barcodes" type="text" label="Barcodes to use" help="Comma separated list of barcodes to use. By default all barcodes in the 'Barcodes index' are used." /> 39 <param name="barcodes" type="text" label="Barcodes to use" help="Comma separated list of barcodes to use. By default all barcodes in the 'Barcodes index' are used." />
40 <param name="trim_barcode" type="select" label="Trim the barcode" help="By default barcodes are trimmed from the resulting splitted datasets"> 40 <param name="trim_barcode" type="select" label="Trim the barcode" help="By default barcodes are trimmed from the resulting split datasets">
41 <option value="" selected="true">Yes</option> 41 <option value="" selected="true">Yes</option>
42 <option value="--keep-barcode">No</option> 42 <option value="--keep-barcode">No</option>
43 </param> 43 </param>
44 <param name="max_distance" type="integer" size="3" value="2" label="Number of allowed polymorphisms" help="Max Levenshtein's distance when looking for mutated barcodes." /> 44 <param name="max_distance" type="integer" size="3" value="2" label="Number of allowed polymorphisms" help="Max Levenshtein's distance when looking for mutated barcodes." />
45 </inputs> 45 </inputs>
46 46
47 <outputs> 47 <outputs>
48 <data format="interval" name="output1" /> 48 <data format="tabular" name="output1" />
49 </outputs> 49 </outputs>
50 <help> 50 <help>
51 51
52 **What it does** 52 **What it does**
53 53
54 This tool splits FASTQ or FASTA datasets into several datasets, using barcodes as the split criteria. 54 This tool splits FASTQ or FASTA datasets into several datasets, using barcodes as the split criteria.
55 55
78 78
79 This tool is based on `ngs-tools`__ by Carlos Borroto &lt;carlos.borroto@gmail.com&gt;. 79 This tool is based on `ngs-tools`__ by Carlos Borroto &lt;carlos.borroto@gmail.com&gt;.
80 80
81 .. __: https://github.com/cjav/ngs-tools/ 81 .. __: https://github.com/cjav/ngs-tools/
82 82
83 </help> 83 </help>
84 </tool> 84 </tool>