Mercurial > repos > jdv > b2b_sync_reads
comparison sync_reads.xml @ 0:6466424fc8ac draft
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
author | jdv |
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date | Wed, 17 Jul 2019 17:48:50 -0400 |
parents | |
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 |