Mercurial > repos > rnateam > bctools

comparison flexbar_dsc.xml @ 46:fd42c7f0ad4b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author rnateam
date Fri, 18 Dec 2015 10:16:27 -0500
parents 0df572b4d644
children
comparison
equal deleted inserted replaced
45:0df572b4d644 46:fd42c7f0ad4b
4 <!-- Modified by Daniel Maticzka --> 4 <!-- Modified by Daniel Maticzka -->
5 <!-- * changed dependency to use separate flexbar package --> 5 <!-- * changed dependency to use separate flexbar package -->
6 <!-- * use paired-end dataset collection as output --> 6 <!-- * use paired-end dataset collection as output -->
7 7
8 <!-- * currently only works for barcode splitting with paired-end reads --> 8 <!-- * currently only works for barcode splitting with paired-end reads -->
9 <!-- * output is fixed to fastqsanger -->
9 10
10 <tool id="flexbardsc" name="Flexbar DSC" version="2.5"> 11 <tool id="flexbardsc" name="Flexbar DSC" version="2.5">
11 12
12 <description>flexible barcode and adapter removal (data set collections)</description> 13 <description>flexible barcode and adapter removal (data set collections)</description>
13 14
429 <!-- Use named regex group to grab pattern 430 <!-- Use named regex group to grab pattern
430 <identifier_0>_<identifier_1>.fq. Here identifier_0 is the list 431 <identifier_0>_<identifier_1>.fq. Here identifier_0 is the list
431 identifier in the nested collection and identifier_1 is either 432 identifier in the nested collection and identifier_1 is either
432 forward or reverse (for instance samp1_forward.fq). 433 forward or reverse (for instance samp1_forward.fq).
433 --> 434 -->
434 <discover_datasets pattern="FlexbarOutput_barcode_(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastq" metadata_source="reads" visible="true" ext="reads.ext"/> 435 <discover_datasets pattern="FlexbarOutput_barcode_(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastq" metadata_source="reads" visible="true" ext="fastqsanger"/>
435 </collection> 436 </collection>
436 </outputs> 437 </outputs>
437 438
438 439
439 <help> 440 <help>