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comparison defuse_bamfastq.xml @ 11:b22f8634ff84 draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
author jjohnson
date Sun, 17 Jan 2016 14:11:06 -0500
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10:f65857c1b92e 11:b22f8634ff84
1 <?xml version="1.0"?>
2 <tool id="defuse_bamfastq" name="Defuse BamFastq" version="@DEFUSE_VERSION@.1">
3 <description>converts a bam file to fastq files.</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <requirements>
8 <expand macro="defuse_requirement" />
9 </requirements>
10 <command>bamfastq
11 #if $pair == True :
12 $pair
13 #end if
14 #if $multiple == True :
15 $multiple
16 #end if
17 #if $rename == True :
18 $rename
19 #end if
20 -b $bamfile
21 -1 $fastq1
22 -2 $fastq2
23 </command>
24 <inputs>
25 <param name="bamfile" type="data" format="bam" label="Bam file"/>
26 <param name="pair" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Name contains pair info as /1 /2."/>
27 <param name="multiple" type="boolean" truevalue="-m" falsevalue="" checked="true" label="Bam contains multiple mappings per read."/>
28 <param name="rename" type="boolean" truevalue="-r" falsevalue="" checked="true" label="Rename with integer IDs."/>
29 </inputs>
30 <stdio>
31 <exit_code range="1:" level="fatal" description="Error" />
32 </stdio>
33 <outputs>
34 <data format="fastqsanger" name="fastq1" label="fastq1" />
35 <data format="fastqsanger" name="fastq2" label="fastq2" />
36 </outputs>
37 <tests>
38 <test>
39 <param name="bamfile" ftype="bam" value="tophat_out2h.bam" />
40 <param name="pair" value="True" />
41 <param name="multiple" value="True" />
42 <param name="rename" value="True" />
43 <output name="fastq1">
44 <assert_contents>
45 <has_text text="@test_mRNA_36_146_27/1" />
46 <not_has_text text="@test_mRNA_36_146_27/2" />
47 <not_has_text text="test_mRNA_150_290_0" />
48 </assert_contents>
49 </output>
50 <output name="fastq2">
51 <assert_contents>
52 <has_text text="@test_mRNA_36_146_27/2" />
53 <not_has_text text="@test_mRNA_36_146_27/1" />
54 <not_has_text text="test_mRNA_150_290_0" />
55 </assert_contents>
56 </output>
57 </test>
58 </tests>
59 <help>
60 bamfastq converts a bam file input into a pair of fastq files that can be used as input to deFuse.
61 </help>
62 <expand macro="citations"/>
63 </tool>