Mercurial > repos > cjav > split_by_barcode
annotate ngs-tools_split_by_barcode.xml @ 2:ee8699b10e83 draft default tip
Updated to use ngs-tools 0.1.8 with better exception handling and proper writing of error messages to sdterr.
author | cjav |
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date | Tue, 15 Oct 2013 13:08:50 -0400 |
parents | 84df983ce1a8 |
children |
rev | line source |
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0 | 1 <tool id="ngs-tools_split_by_barcode" name="Barcode Splitter (ngs-tools)" force_history_refresh="True" version="1.0.1"> |
2 <description></description> | |
3 <requirements> | |
2
ee8699b10e83
Updated to use ngs-tools 0.1.8 with better exception handling and proper writing of error messages to sdterr.
cjav
parents:
0
diff
changeset
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4 <requirement type="package" version="0.1.8">ngs-tools</requirement> |
0 | 5 </requirements> |
6 <command> | |
7 ngs-tools split-by-barcode | |
8 $trim_barcode $input_format.format | |
9 --barcode-size $barcode_length --max-distance $max_distance | |
10 #if $barcodes | |
11 --barcodes $barcodes | |
12 #end if | |
13 --report $output1 --galaxy $output1.id --output $__new_file_path__ | |
14 $barcode_index | |
15 #for $i in $input_format.inputs | |
16 ${i.input} | |
17 #end for | |
18 </command> | |
19 | |
20 <inputs> | |
21 <conditional name="input_format"> | |
22 <param name="format" type="select" label="Input format"> | |
23 <option value="--fastq" selected="true">Fastq</option> | |
24 <option value="">Fasta</option> | |
25 </param> | |
26 <when value="--fastq"> | |
27 <repeat name="inputs" title="Dataset" help="Datasets to split."> | |
28 <param name="input" type="data" label="Dataset to split" format="fastq,fastqsanger,fastqsolexa,fastqillumina" /> | |
29 </repeat> | |
30 </when> | |
31 <when value=""> | |
32 <repeat name="inputs" title="Dataset" help="Datasets to split."> | |
33 <param name="input" type="data" label="Dataset to split" format="fasta" /> | |
34 </repeat> | |
35 </when> | |
36 </conditional> | |
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." /> | |
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." /> | |
2
ee8699b10e83
Updated to use ngs-tools 0.1.8 with better exception handling and proper writing of error messages to sdterr.
cjav
parents:
0
diff
changeset
|
40 <param name="trim_barcode" type="select" label="Trim the barcode" help="By default barcodes are trimmed from the resulting split datasets"> |
0 | 41 <option value="" selected="true">Yes</option> |
42 <option value="--keep-barcode">No</option> | |
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." /> | |
45 </inputs> | |
46 | |
47 <outputs> | |
2
ee8699b10e83
Updated to use ngs-tools 0.1.8 with better exception handling and proper writing of error messages to sdterr.
cjav
parents:
0
diff
changeset
|
48 <data format="tabular" name="output1" /> |
0 | 49 </outputs> |
2
ee8699b10e83
Updated to use ngs-tools 0.1.8 with better exception handling and proper writing of error messages to sdterr.
cjav
parents:
0
diff
changeset
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50 <help> |
0 | 51 |
52 **What it does** | |
53 | |
54 This tool splits FASTQ or FASTA datasets into several datasets, using barcodes as the split criteria. | |
55 | |
56 -------- | |
57 | |
58 **Barcode index format** | |
59 | |
60 Barcode index datasets are simple tab separated files. | |
61 Each line should contain an identifier (descriptive name for the barcode), and the barcode itself (A/C/G/T), separated by a TAB character. | |
62 Example:: | |
63 | |
64 RL001 ACACGACGACT | |
65 RL002 ACACGTAGTAT | |
66 RL003 ACACTACTCGT | |
67 RL004 ACGACACGTAT | |
68 RL005 ACGAGTAGACT | |
69 | |
70 For each barcode, a new FASTQ or FASTA dataset will be created (with the barcode's identifier as part of the dataset name). | |
71 Sequences matching the barcode will be stored in the appropriate dataset. | |
72 | |
73 One additional FASTQ or FASTA dataset will be created (the 'Unassigned' dataset), where sequences not matching any barcode will be stored. | |
74 | |
75 The output of this tool is one history dataset per each barcode provided plus a report with the split counts. | |
76 | |
77 ------ | |
78 | |
79 This tool is based on `ngs-tools`__ by Carlos Borroto <carlos.borroto@gmail.com>. | |
80 | |
81 .. __: https://github.com/cjav/ngs-tools/ | |
82 | |
2
ee8699b10e83
Updated to use ngs-tools 0.1.8 with better exception handling and proper writing of error messages to sdterr.
cjav
parents:
0
diff
changeset
|
83 </help> |
0 | 84 </tool> |