Mercurial > repos > cjav > split_by_barcode
annotate ngs-tools_split_by_barcode.xml @ 6:9b59d2017dd6 draft
Now using ngs-tools 0.1.6.
| author | cjav |
|---|---|
| date | Wed, 18 Sep 2013 16:28:27 -0400 |
| parents | 1506445d0665 |
| children | 9fa7fd4d78bb |
| rev | line source |
|---|---|
|
5
1506445d0665
New way of providing barcodes to use. Using ngs-tools==0.1.5.
cjav
parents:
4
diff
changeset
|
1 <tool id="ngs-tools_split_by_barcode" name="Barcode Splitter (ngs-tools)" force_history_refresh="True" version="1.0.1"> |
| 1 | 2 <description></description> |
| 3 | 3 <requirements> |
| 6 | 4 <requirement type="package" version="0.1.6">ngs-tools</requirement> |
| 3 | 5 </requirements> |
| 1 | 6 <command> |
| 7 ngs-tools split-by-barcode | |
| 4 | 8 $trim_barcode $input_format.format |
| 1 | 9 --barcode-size $barcode_length --max-distance $max_distance |
|
5
1506445d0665
New way of providing barcodes to use. Using ngs-tools==0.1.5.
cjav
parents:
4
diff
changeset
|
10 #if $barcodes |
|
1506445d0665
New way of providing barcodes to use. Using ngs-tools==0.1.5.
cjav
parents:
4
diff
changeset
|
11 --barcodes $barcodes |
|
1506445d0665
New way of providing barcodes to use. Using ngs-tools==0.1.5.
cjav
parents:
4
diff
changeset
|
12 #end if |
| 1 | 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> | |
| 2 | 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." /> | |
| 1 | 38 <param name="barcode_length" type="integer" size="3" value="11" label="Barcode length" help="Please specify the barcode length." /> |
|
5
1506445d0665
New way of providing barcodes to use. Using ngs-tools==0.1.5.
cjav
parents:
4
diff
changeset
|
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." /> |
| 4 | 40 <param name="trim_barcode" type="select" label="Trim the barcode" help="By default barcodes are trimmed from the resulting splitted datasets"> |
| 41 <option value="" selected="true">Yes</option> | |
| 42 <option value="--keep-barcode">No</option> | |
| 1 | 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> | |
| 48 <data format="interval" name="output1" /> | |
| 49 </outputs> | |
| 50 <help> | |
| 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 | |
| 83 </help> | |
| 84 </tool> |