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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
author ebi-gxa
date Thu, 17 Mar 2022 01:46:15 +0000
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1 <tool id="fastq_pair" name="Paired-end fastq pairer" profile="18.01" version="1.0+galaxy0">
2 <description>Rewrite paired-end fastq files to make sure that all reads have a mate and to separate out singletons.</description>
3 <requirements>
4 <requirement type="package" version="1.0">fastq-pair</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7
8 ## Unzip gzipped inputs
9 #if $fastq1.is_of_type("fastqsanger.gz"):
10 gzip -d -c '$fastq1' > 1.fq &&
11 #else:
12 mv '$fastq1' 1.fq &&
13 #end if
14
15 #if $fastq2.is_of_type("fastqsanger.gz"):
16 gzip -d -c '$fastq2' > 2.fq &&
17 #else:
18 mv '$fastq2' 2.fq &&
19 #end if
20
21
22 ## Run fastq_pair
23 fastq_pair
24
25 #if $table_size:
26 -t '$table_size'
27 #end if
28
29 #if $print_elements:
30 -p '$print_elements'
31 #end if
32
33 #if $verbose:
34 '$verbose'
35 #end if
36
37 1.fq 2.fq
38
39 ## Compress outputs
40 #if $compress == "yes":
41 ; gzip 1.fq.paired.fq
42 ; gzip 2.fq.paired.fq
43 ; gzip 1.fq.single.fq
44 ; gzip 2.fq.single.fq
45 #end if
46
47 ]]></command>
48 <inputs>
49 <param name="verbose" label="Verbose" optional="true" value="false" argument="-v" type="boolean" truevalue="-v" falsevalue="" checked="true" help="Verbose output. This is mainly for debugging." />
50 <param name="fastq1" label="FASTQ file 1" type="data" format="fastqsanger,fastqsanger.gz" optional="false" help="FASTQ file input, file 1 of pair" />
51 <param name="fastq2" label="FASTQ file 2" type="data" format="fastqsanger,fastqsanger.gz" optional="false" help="FASTQ file input, file 2 of pair" />
52 <param name="table_size" label="Table size" argument="-t" optional="true" value="100003" type="integer" help="Table size (default 100003)" />
53 <param name="print_elements" label="Number elements to print" argument="-p" type="integer" optional="true" help="Print this number of elements in each bucket in the table." />
54 <param name="compress" label="Compress outputs?" type="boolean" optional="true" value="true" truevalue="yes" falsevalue="no" checked="false" help="Check if outputs should be compressed (.gz)" />
55 </inputs>
56 <outputs>
57 <collection name="uncompressed" type="list" format="fastqsanger" label="${tool.name} on ${on_string}: Paired reads and singletons">
58 <filter>compress == False</filter>
59 <data name="fwd_paired" from_work_dir="1.fq.paired.fq"/>
60 <data name="rev_paired" from_work_dir="2.fq.paired.fq"/>
61 <data name="fwd_single" from_work_dir="1.fq.single.fq"/>
62 <data name="rev_single" from_work_dir="2.fq.single.fq"/>
63 </collection>
64 <collection name="compressed" type="list" format="fastqsanger.gz" label="${tool.name} on ${on_string}: Paired reads and singletons, compressed">
65 <filter>compress</filter>
66 <data name="fwd_paired_gz" from_work_dir="1.fq.paired.fq.gz"/>
67 <data name="rev_paired_gz" from_work_dir="2.fq.paired.fq.gz"/>
68 <data name="fwd_single_gz" from_work_dir="1.fq.single.fq.gz"/>
69 <data name="rev_single_gz" from_work_dir="2.fq.single.fq.gz"/>
70 </collection>
71 </outputs>
72 <tests>
73 <test>
74 <param name="table_size" value="1000"/>
75 <param name="fastq1" value="left.fastq"/>
76 <param name="fastq2" value="right.fastq"/>
77 <output_collection name="uncompressed" type="list" count="4">
78 <element name="fwd_paired" ftype="fastqsanger">
79 <assert_contents><has_line_matching expression="^@GFH7CG303GRT2I/1[ -~]+" /></assert_contents>
80 </element>
81 <element name="rev_paired" ftype="fastqsanger">
82 <assert_contents><has_line_matching expression="^@GFH7CG303GRT2I/2[ -~]+" /></assert_contents>
83 </element>
84 <element name="fwd_single" ftype="fastqsanger">
85 <assert_contents><has_line_matching expression="^@GFH7CG303GGIBL/1[ -~]+" /></assert_contents>
86 </element>
87 <element name="rev_single" ftype="fastqsanger">
88 <assert_contents><has_line_matching expression="^@GFH7CG303GSASH/2[ -~]+" /></assert_contents>
89 </element>
90 </output_collection>
91 </test>
92 <test>
93 <param name="table_size" value="1000"/>
94 <param name="fastq1" value="left.fastq.gz"/>
95 <param name="fastq2" value="right.fastq.gz"/>
96 <param name="compress" value="true"/>
97 <output_collection name="compressed" type="list" count="4">
98 <element name="fwd_paired_gz" ftype="fastqsanger.gz">
99 <assert_contents><has_size value="16000" delta="1600"/></assert_contents>
100 </element>
101 <element name="rev_paired_gz" ftype="fastqsanger.gz">
102 <assert_contents><has_size value="16000" delta="1600"/></assert_contents>
103 </element>
104 <element name="fwd_single_gz" ftype="fastqsanger.gz">
105 <assert_contents><has_size value="62000" delta="6200"/></assert_contents>
106 </element>
107 <element name="rev_single_gz" ftype="fastqsanger.gz">
108 <assert_contents><has_size value="8500" delta="850"/></assert_contents>
109 </element>
110 </output_collection>
111 </test>
112 </tests>
113 <help><![CDATA[
114 =======================================================
115 Paired-end fastq pairer (fastq_pair)
116 =======================================================
117
118 Match up paired end fastq files quickly and efficiently.
119 This galaxy tool can accept gzipped fastq files.
120
121 OPTIONS
122 -t table size (default 100003)
123 -p print the number of elements in each bucket in the table
124 -v verbose output. This is mainly for debugging
125 ]]></help>
126 <citations>
127 <citation type="doi">10.1101/552885</citation>
128 </citations>
129 </tool>