Mercurial > repos > jjohnson > ubu_sam2fastq

comparison ubu_sam2fastq.xml @ 0:aa2cf6718319 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jjohnson
date Mon, 02 Nov 2015 08:48:24 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:aa2cf6718319
1 <tool id="ubu_sam2fastq" name="UBU sam2fastq" version="0.1.0">
2 <description>Convert a SAM/BAM file to FASTQ</description>
3
4 <requirements>
5 <requirement version="1.2">ubu</requirement>
6 </requirements>
7 <stdio>
8 <exit_code range="1:" />
9 </stdio>
10
11 <command><![CDATA[
12 java -Xmx1G -jar \$UBU_JAR sam2fastq --in $input --fastq1 paired1.fastq --fastq2 paired2.fastq --end1 '$end1' --end2 '$end2'
13 ]]></command>
14 <inputs>
15 <param name="input" type="data" format="sam,bam" label="Sam or Bam file to convert" />
16 <param name="end1" type="text" value="/1" label="Id suffix used to identify the first read in a pair." />
17 <param name="end2" type="text" value="/2" label="Id suffix used to identify the second read in a pair." />
18 </inputs>
19 <outputs>
20 <data name="fastq1" format="data" from_work_dir="paired1.fastq" />
21 <data name="fastq2" format="data" from_work_dir="paired2.fastq" />
22 </outputs>
23 <tests>
24 <test>
25 <param name="input" value="sam2fastq_test.sam" />
26 <output name="fastq1" file="sam2fastq_expected_paired1.fastq"/>
27 <output name="fastq2" file="sam2fastq_expected_paired2.fastq"/>
28 </test>
29 </tests>
30 <help><![CDATA[
31 input SAM/BAM file
32 Option Description
33 ------ -----------
34 --in Required input sam or bam file
35 --fastq1 Required output FASTQ file
36 --fastq2 Second FASTQ file for paired end
37 --end1 Id suffix used to identify the first
38 read in a pair. i.e. /1 (omit this
39 option to use bit flag)
40 --end2 Id suffix used to identify the second
41 read in a pair. i.e. /2 (omit this
42 option to use bit flag)
43
44 ]]></help>
45 </tool>