Mercurial > repos > jdv > b2b_sync_reads

comparison sync_reads.xml @ 0:6466424fc8ac draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
author jdv
date Wed, 17 Jul 2019 17:48:50 -0400
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children b7f66945bf72
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1 <tool id="b2b_sync_reads" name="Sync paired reads" version="0.004">
2
3 <description>Synchronize trimmed/filtered read-pair set</description>
4
5 <!-- ***************************************************************** -->
6
7 <requirements>
8 <!-- <requirement type="package" version="0.003">b2b-utils</requirement> -->
9 <requirement type="package" version="0.006007">perl-biox-seq</requirement>
10 </requirements>
11
12 <!-- ***************************************************************** -->
13
14 <version_command>sync_reads --version | perl -wnE'print "$1\n" for /sync_reads v(.+)/g'</version_command>
15
16 <!-- ***************************************************************** -->
17
18 <command detect_errors="aggressive">
19 <![CDATA[
20
21 sync_reads
22 --fwd $input1
23 --rev $input2
24 --fwd_out $fwd_out
25 --rev_out $rev_out
26 #if str($write_singles) == 'y':
27 --singles
28 --fwd_singles_out $fwd_s_out
29 --rev_singles_out $rev_s_out
30 #end if
31
32 ]]>
33 </command>
34
35 <!-- ***************************************************************** -->
36
37 <inputs>
38
39 <param name="job_name" type="text" size="120" value="sync_reads" label="Job narrative (added to output names)"
40 help="Only letters, numbers and underscores (_) will be retained in this field">
41 <sanitizer invalid_char="">
42 <valid initial="string.letters,string.digits"><add value="_" /> </valid>
43 </sanitizer>
44 </param>
45 <!-- FASTQ input(s) and options specifically for paired-end data. -->
46 <param name="input1" format="fastqsanger,fastq" type="data" label="Forward read FASTQ file" help="Forward read FASTQ file"/>
47 <param name="input2" format="fastqsanger,fastq" type="data" label="Reverse read FASTQ file" help="Reverse read FASTQ file"/>
48 <param name="write_singles" type="boolean" label="Output singletons" checked="False" truevalue="y" falsevalue="n" />
49
50 </inputs>
51
52 <!-- ***************************************************************** -->
53
54 <outputs>
55 <data format_source="input1" name="fwd_out" label="${job_name}_sync.1.fq" />
56 <data format_source="input2" name="rev_out" label="${job_name}_sync.2.fq" />
57 <data format_source="input1" name="fwd_s_out" label="${job_name}_singles.1.fq">
58 <filter>write_singles</filter>
59 </data>
60 <data format_source="input2" name="rev_s_out" label="${job_name}_singles.2.fq">
61 <filter>write_singles</filter>
62 </data>
63 </outputs>
64
65 <!-- ***************************************************************** -->
66
67 <tests>
68
69 <test>
70 <param name="input1" value="test_R1.fq" ftype="fastq" />
71 <param name="input2" value="test_R2.fq" ftype="fastq" />
72 <output name="fwd_out" file="test_R1.sync.fq" compare="diff" />
73 <output name="rev_out" file="test_R2.sync.fq" compare="diff" />
74 </test>
75
76 <test>
77 <param name="input1" value="test_R1.fq" ftype="fastq" />
78 <param name="input2" value="test_R2.fq" ftype="fastq" />
79 <param name="write_singles" value="True" />
80 <output name="fwd_out" file="test_R1.sync.fq" compare="diff" />
81 <output name="rev_out" file="test_R2.sync.fq" compare="diff" />
82 <output name="fwd_s_out" file="test_R1.singles.fq" compare="diff" />
83 <output name="rev_s_out" file="test_R2.singles.fq" compare="diff" />
84 </test>
85
86 </tests>
87
88 <!-- ***************************************************************** -->
89
90 <help>
91
92 sync_reads is a utility from b2b-utils for synchronizing a pair of forward and
93 reverse FASTQ read files. It will output a new pair of files containing only
94 read pairs found in both input files. It can optionally output singletons from
95 each input file as well.
96
97 </help>
98
99 <!-- ***************************************************************** -->
100
101 <citations>
102 </citations>
103
104 </tool>
105