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comparison bamToFastq.xml @ 18:5efc48568d8d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
author iuc
date Tue, 13 Oct 2015 17:20:34 -0400
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17:a2d4c30ba2f9 18:5efc48568d8d
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 $tags
11 -i '$input'
12 -fq '$output'
13 #if $fq2:
14 -fq2 '$output2'
15 #end if
16 </command>
17 <inputs>
18 <param format="bam" name="input" type="data" label="Convert the following BAM file to FASTQ"/>
19 <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."/>
20 <param name="fq2" type="boolean" truevalue="-fq2" falsevalue="" selected="False" label="FASTQ for second end.
21 Used if BAM contains paired-end data. BAM should be sorted by query name if creating paired FASTQ with this option."/>
22 </inputs>
23 <outputs>
24 <data format="fastq" name="output" metadata_source="input" label="${input.name} (as FASTQ)"/>
25 <data format="fastq2" name="output2" metadata_source="input" label="${input.name} (as FASTQ)">
26 <filter>fq2 is True</filter>
27 </data>
28 </outputs>
29 <help>
30
31 **What it does**
32
33 bedtools bamtofastq is a conversion utility for extracting FASTQ records from sequence alignments in BAM format.
34
35 @REFERENCES@
36
37 </help>
38 <expand macro="citations" />
39 </tool>