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comparison bamToFastq.xml @ 0:4fb5ea02b441 draft

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author iuc
date Tue, 15 Jul 2014 14:42:23 -0400
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1 <tool id="bedtools_bamtofastq" name="Convert from BAM to FastQ" version="@WRAPPER_VERSION@.0">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <command>
9 bedtools bamtofastq
10 $tags
11 $fq2
12 -i '$input'
13 -fq '$output'
14 </command>
15 <inputs>
16 <param format="bam" name="input" type="data" label="Convert the following BAM file to FASTQ"/>
17 <param name="tags" type="boolean" truevalue="-tags" falsevalue="" selected="False" label="Create FASTQ based on the mate info in the BAM R2 and Q2 tags."/>
18 <param name="fq2" type="boolean" truevalue="-fq2" falsevalue="" selected="False" label="ASTQ for second end. Used if BAM contains paired-end data. BAM should be sorted by query name if creating paired FASTQ with this option."/>
19 </inputs>
20 <outputs>
21 <data format="fastq" name="output" metadata_source="input" label="${input.name} (as FASTQ)"/>
22 </outputs>
23 <help>
24
25 **What it does**
26
27 bedtools bamtofastq is a conversion utility for extracting FASTQ records from sequence alignments in BAM format.
28
29 @REFERENCES@
30
31 </help>
32 </tool>