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comparison extract_bcs.xml @ 5:e841de88235c draft

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author rnateam
date Fri, 23 Oct 2015 07:28:06 -0400
parents bf5b606f1aa7
children 1bfc5a5de843
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4:d03c001f7c73 5:e841de88235c
1 <tool id="extract_bcs.py" name="extract_bcs.py" version="0.1.0"> 1 <tool id="extract_bcs.py" name="extract_bcs.py" version="1.0.0">
2 <description>Extract barcodes using pattern.</description> 2 <description>Extract barcodes using pattern.</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
14 14
15 #if $positional_2 and $positional_2 is not None: 15 #if $positional_2 and $positional_2 is not None:
16 $positional_2 16 $positional_2
17 #end if 17 #end if
18 18
19 --bcs $extractedbcs
20
19 > $default]]></command> 21 > $default]]></command>
20 <inputs> 22 <inputs>
21 <param area="false" label="Barcoded sequences." name="positional_1" type="data" format="fastq"/> 23 <param area="false" label="Barcoded sequences." name="positional_1" type="data" format="fastq"/>
22 <param area="false" label="Pattern of barcode nucleotides starting at 5'-end. X positions will be moved to the header, N positions will be kept." name="positional_2" type="text"/> 24 <param area="false" label="Pattern of barcode nucleotides starting at 5'-end. X positions will be moved to the header, N positions will be kept." name="positional_2" type="text"/>
23 </inputs> 25 </inputs>
24 <outputs> 26 <outputs>
25 <data hidden="false" name="default" format="fastq" /> 27 <data hidden="false" name="default" format="fastq"/>
28 <data name="extractedbcs" format="fasta"/>
26 </outputs> 29 </outputs>
27 <tests> 30 <tests>
28 <test> 31 <test>
29 <param name="positional_1" value="reads.fastq"/> 32 <param name="positional_1" value="reads.fastq"/>
30 <param name="positional_2" value="XXXNNXXX"/> 33 <param name="positional_2" value="XXXNNXXX"/>
31 <output name="default" file="result.fastq"/> 34 <output name="default" file="result_original_head.fastq"/>
35 <output name="extractedbcs" file="result.fa"/>
32 </test> 36 </test>
33 </tests> 37 </tests>
34 <help><![CDATA[ 38 <help><![CDATA[
35 Exract barcodes from a FASTQ file according to a user-specified pattern. 39 Exract barcodes from a FASTQ file according to a user-specified pattern.
36 40