Mercurial > repos > iuc > presto_pairseq

comparison presto_pairseq.xml @ 3:49e7407445c3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit d52e3c9c53dd358e14e65a3a083e7d5c102f8697"
author iuc
date Sat, 25 Sep 2021 18:34:52 +0000
parents 7bdff30820bf
children eed465eb14a3
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2:7bdff30820bf 3:49e7407445c3
1 <tool id="presto_pairseq" name="pRESTO PairSeq" version="@TOOL_VERSION@"> 1 <tool id="presto_pairseq" name="pRESTO PairSeq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Sorts and matches sequence records with matching coordinates across files</description> 2 <description>Sorts and matches sequence records with matching coordinates across files</description>
3 3 <expand macro="bio_tools"/>
4 <macros> 4 <macros>
5 <import>presto_macros.xml</import> 5 <import>presto_macros.xml</import>
6 </macros> 6 </macros>
7 7
8 <expand macro="requirements"/> 8 <expand macro="requirements"/>
9 9
10 <version_command>PairSeq.py --version</version_command> 10 <version_command>PairSeq.py --version</version_command>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 ln -s '$r1_in' r1.fastq && 12 ln -s '$r1_in' r1.fastq &&
13 ln -s '$r2_in' r2.fastq && 13 ln -s '$r2_in' r2.fastq &&
14 PairSeq.py 14 PairSeq.py
19 --1f $r1_annotations 19 --1f $r1_annotations
20 #end if 20 #end if
21 #if $r2_annotations 21 #if $r2_annotations
22 --2f $r2_annotations 22 --2f $r2_annotations
23 #end if 23 #end if
24 $failed
24 --outdir=. 25 --outdir=.
25 --outname=tmp 26 --outname=tmp
26 ]]></command> 27 ]]></command>
27 <inputs> 28 <inputs>
28 <param argument="-1" name="r1_in" type="data" format="fastq" label="Read 1 FASTQ/FASTA file."/> 29 <param argument="-1" name="r1_in" type="data" format="fastq" label="Read 1 FASTQ/FASTA file."/>
32 </param> 33 </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 <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 <expand macro="text-regex-validator"/>
35 </param> 36 </param>
36 <expand macro="presto-coord-param"/> 37 <expand macro="presto-coord-param"/>
38 <param argument="--failed" type="boolean" checked="false" truevalue="--failed" falsevalue="" label="Failed reads fastq output" />
37 </inputs> 39 </inputs>
38 <outputs> 40 <outputs>
39 <data name="r1_out" format="fastq" from_work_dir="tmp-1_pair-pass.fastq"/> 41 <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"/> 42 <data name="r2_out" format="fastq" from_work_dir="tmp-2_pair-pass.fastq"/>
43 <!-- only give these 2 outputs if input failed_fastq=True-->
44 <data name="r1_fail_out" format="fastq" from_work_dir="tmp-1_pair-fail.fastq">
45 <filter>failed</filter>
46 </data>
47 <data name="r2_fail_out" format="fastq" from_work_dir="tmp-2_pair-fail.fastq">
48 <filter>failed</filter>
49 </data>
41 </outputs> 50 </outputs>
42
43 <tests> 51 <tests>
44 <test> 52 <test expect_num_outputs="2">
45 <param name="r1_in" value="presto_pairseq_test1_r1_in.fastq"/> 53 <param name="r1_in" value="presto_pairseq_test1_r1_in.fastq"/>
46 <param name="r2_in" value="presto_pairseq_test1_r2_in.fastq"/> 54 <param name="r2_in" value="presto_pairseq_test1_r2_in.fastq"/>
47 <param name="r2_annotations" value="BARCODE"/> 55 <param name="r2_annotations" value="BARCODE"/>
48 <param name="coord" value="illumina"/> 56 <param name="coord" value="illumina"/>
49 <output name="r1_out" file="presto_pairseq_test1_r1_out.fastq" sort="true"/> 57 <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"/> 58 <output name="r2_out" file="presto_pairseq_test1_r2_out.fastq" sort="true"/>
51 </test> 59 </test>
60 <test expect_num_outputs="4">
61 <param name="r1_in" value="presto_pairseq_test1_r1_in.fastq"/>
62 <param name="r2_in" value="presto_pairseq_test1_r2_in.fastq"/>
63 <param name="r2_annotations" value="BARCODE"/>
64 <param name="coord" value="illumina"/>
65 <param name="failed" value="true"/>
66 <output name="r1_out" file="presto_pairseq_test1_r1_out.fastq" sort="true"/>
67 <output name="r2_out" file="presto_pairseq_test1_r2_out.fastq" sort="true"/>
68 <output name="r1_fail_out">
69 <assert_contents>
70 <has_text text="@"/>
71 </assert_contents>
72 </output>
73 <output name="r2_fail_out">
74 <assert_contents>
75 <has_text text="@"/>
76 </assert_contents>
77 </output>
78 </test>
52 </tests> 79 </tests>
53
54 <help><![CDATA[ 80 <help><![CDATA[
55 Sorts and matches sequence records with matching coordinates across files. 81 Sorts and matches sequence records with matching coordinates across files.
56 82
57 See the `pRESTO online help <@PRESTO_BASE_URL@/en/stable>`_ for more information. 83 See the `pRESTO online help <@PRESTO_BASE_URL@/en/stable>`_ for more information.
58 84