Mercurial > repos > jvolkening > b2b_sync_reads

comparison sync_reads.xml @ 0:c97a821e54f3 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
author jvolkening
date Sat, 02 Mar 2024 07:44:26 +0000
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children e8df16b34fec
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1 <tool id="b2b_sync_reads" name="Sync paired reads" version="0.005">
2
3 <description>Synchronize trimmed/filtered read-pair set</description>
4
5 <!-- ***************************************************************** -->
6
7 <requirements>
8 <requirement type="package" version="0.019">b2b-utils</requirement>
9 </requirements>
10
11 <!-- ***************************************************************** -->
12
13 <version_command>sync_reads --version | perl -wnE'print "$1\n" for /sync_reads v(.+)/g'</version_command>
14
15 <!-- ***************************************************************** -->
16
17 <command detect_errors="aggressive">
18 <![CDATA[
19
20 sync_reads
21 --fwd $input1
22 --rev $input2
23 --fwd_out $fwd_out
24 --rev_out $rev_out
25 #if str($write_singles) == 'y':
26 --singles
27 --fwd_singles_out $fwd_s_out
28 --rev_singles_out $rev_s_out
29 #end if
30
31 ]]>
32 </command>
33
34 <!-- ***************************************************************** -->
35
36 <inputs>
37
38 <param name="job_name" type="text" size="120" value="sync_reads" label="Job narrative (added to output names)"
39 help="Only letters, numbers and underscores (_) will be retained in this field">
40 <sanitizer invalid_char="">
41 <valid initial="string.letters,string.digits"><add value="_" /> </valid>
42 </sanitizer>
43 </param>
44 <!-- FASTQ input(s) and options specifically for paired-end data. -->
45 <param name="input1" format="fastqsanger,fastq" type="data" label="Forward read FASTQ file" help="Forward read FASTQ file"/>
46 <param name="input2" format="fastqsanger,fastq" type="data" label="Reverse read FASTQ file" help="Reverse read FASTQ file"/>
47 <param name="write_singles" type="boolean" label="Output singletons" checked="False" truevalue="y" falsevalue="n" />
48
49 </inputs>
50
51 <!-- ***************************************************************** -->
52
53 <outputs>
54 <data format_source="input1" name="fwd_out" label="${job_name}_sync.1.fq" />
55 <data format_source="input2" name="rev_out" label="${job_name}_sync.2.fq" />
56 <data format_source="input1" name="fwd_s_out" label="${job_name}_singles.1.fq">
57 <filter>write_singles</filter>
58 </data>
59 <data format_source="input2" name="rev_s_out" label="${job_name}_singles.2.fq">
60 <filter>write_singles</filter>
61 </data>
62 </outputs>
63
64 <!-- ***************************************************************** -->
65
66 <tests>
67
68 <test expect_num_outputs="2">
69 <param name="input1" value="test_R1.fq" ftype="fastq" />
70 <param name="input2" value="test_R2.fq" ftype="fastq" />
71 <output name="fwd_out" file="test_R1.sync.fq" compare="diff" />
72 <output name="rev_out" file="test_R2.sync.fq" compare="diff" />
73 </test>
74
75 <test expect_num_outputs="4">
76 <param name="input1" value="test_R1.fq" ftype="fastq" />
77 <param name="input2" value="test_R2.fq" ftype="fastq" />
78 <param name="write_singles" value="True" />
79 <output name="fwd_out" file="test_R1.sync.fq" compare="diff" />
80 <output name="rev_out" file="test_R2.sync.fq" compare="diff" />
81 <output name="fwd_s_out" file="test_R1.singles.fq" compare="diff" />
82 <output name="rev_s_out" file="test_R2.singles.fq" compare="diff" />
83 </test>
84
85 </tests>
86
87 <!-- ***************************************************************** -->
88
89 <help>
90
91 sync_reads is a utility from b2b-utils for synchronizing a pair of forward and
92 reverse FASTQ read files. It will output a new pair of files containing only
93 read pairs found in both input files. It can optionally output singletons from
94 each input file as well.
95
96 </help>
97
98 <!-- ***************************************************************** -->
99
100 <citations>
101 </citations>
102
103 </tool>
104