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comparison presto_pairseq.xml @ 0:d08bfab1c8fc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
author iuc
date Wed, 30 May 2018 15:34:01 -0400
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-1:000000000000 0:d08bfab1c8fc
1 <tool id="presto_pairseq" name="pRESTO PairSeq" version="@PRESTO_VERSION@">
2 <description>Sorts and matches sequence records with matching coordinates across files</description>
3
4 <macros>
5 <import>presto_macros.xml</import>
6 </macros>
7
8 <expand macro="requirements"/>
9
10 <version_command>PairSeq.py --version</version_command>
11 <command detect_errors="exit_code"><![CDATA[
12 ln -s '$r1_in' r1.fastq &&
13 ln -s '$r2_in' r2.fastq &&
14 PairSeq.py
15 -1 r1.fastq
16 -2 r2.fastq
17 --coord $coord
18 #if $r1_annotations
19 --1f $r1_annotations
20 #end if
21 #if $r2_annotations
22 --2f $r2_annotations
23 #end if
24 --outdir=.
25 --outname=tmp
26 ]]></command>
27 <inputs>
28 <param argument="-1" name="r1_in" type="data" format="fastq" label="Read 1 FASTQ/FASTA file."/>
29 <param argument="-2" name="r2_in" type="data" format="fastq" label="Read 2 FASTQ/FASTA file."/>
30 <param argument="--1f" name="r1_annotations" type="text" optional="true" label="Annotation(s) to copy from R1 to R2." help="Multiple annotation must be space-separated.">
31 <expand macro="text-regex-validator"/>
32 </param>
33 <param argument="--2f" name="r2_annotations" type="text" optional="true" label="Annotation(s) to copy from R2 to R1." help="Multiple annotation must be space-separated.">
34 <expand macro="text-regex-validator"/>
35 </param>
36 <expand macro="presto-coord-param"/>
37 </inputs>
38 <outputs>
39 <data name="r1_out" format="fastq" from_work_dir="tmp-1_pair-pass.fastq"/>
40 <data name="r2_out" format="fastq" from_work_dir="tmp-2_pair-pass.fastq"/>
41 </outputs>
42
43 <tests>
44 <test>
45 <param name="r1_in" value="presto_pairseq_test1_r1_in.fastq"/>
46 <param name="r2_in" value="presto_pairseq_test1_r2_in.fastq"/>
47 <param name="r2_annotations" value="BARCODE"/>
48 <param name="coord" value="illumina"/>
49 <output name="r1_out" file="presto_pairseq_test1_r1_out.fastq" sort="true"/>
50 <output name="r2_out" file="presto_pairseq_test1_r2_out.fastq" sort="true"/>
51 </test>
52 </tests>
53
54 <help><![CDATA[
55 Sorts and matches sequence records with matching coordinates across files.
56
57 See the `pRESTO online help <@PRESTO_URL_BASE@/PairSeq.html>`_ for more information.
58
59 @HELP_NOTE@
60 ]]></help>
61 <expand macro="citations" />
62 </tool>