Mercurial > repos > cjav > split_by_barcode
comparison ngs-tools_split_by_barcode.xml @ 5:1506445d0665 draft
New way of providing barcodes to use. Using ngs-tools==0.1.5.
| author | cjav |
|---|---|
| date | Mon, 16 Sep 2013 14:36:09 -0400 |
| parents | f40640700846 |
| children | 9b59d2017dd6 |
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| 4:f40640700846 | 5:1506445d0665 |
|---|---|
| 1 <tool id="ngs-tools_split_by_barcode" name="Barcode Splitter (ngs-tools)" force_history_refresh="True"> | 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="0.1.4">ngs-tools</requirement> | 4 <requirement type="package" version="0.1.5">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 |
| 10 #for $i in $barcodes | 10 #if $barcodes |
| 11 --barcode ${i.barcode} | 11 --barcodes $barcodes |
| 12 #end for | 12 #end if |
| 13 --report $output1 --galaxy $output1.id --output $__new_file_path__ | 13 --report $output1 --galaxy $output1.id --output $__new_file_path__ |
| 14 $barcode_index | 14 $barcode_index |
| 15 #for $i in $input_format.inputs | 15 #for $i in $input_format.inputs |
| 16 ${i.input} | 16 ${i.input} |
| 17 #end for | 17 #end for |
| 34 </repeat> | 34 </repeat> |
| 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 <repeat name="barcodes" title="Barcode" help="Barcodes to use. By default all barcodes with the correct length in the index are used. By using this option you can limit which ones to use."> | 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="barcode" type="text" label="Barcode to use" /> | |
| 41 </repeat> | |
| 42 <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 splitted datasets"> |
| 43 <option value="" selected="true">Yes</option> | 41 <option value="" selected="true">Yes</option> |
| 44 <option value="--keep-barcode">No</option> | 42 <option value="--keep-barcode">No</option> |
| 45 </param> | 43 </param> |
| 46 <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." /> |