Mercurial > repos > jvolkening > b2b_fq_interleave

comparison fq_interleave.xml @ 0:6530b8a73225 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
author jvolkening
date Fri, 08 Mar 2024 00:48:17 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:6530b8a73225
1 <tool id="b2b_@TOOL_NAME@" name="Interleave reads"
2 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT" profile="20.01">
3 <description>Interleaved paired FASTQ files</description>
4 <macros>
5 <token name="@TOOL_NAME@">fq_interleave</token>
6 <token name="@TOOL_VERSION@">0.202</token>
7 <token name="@VERSION_SUFFIX@">1</token>
8 <import>macros.xml</import>
9 </macros>
10 <edam_topics>
11 <edam_topic>topic_0080</edam_topic> <!-- Sequence analysis -->
12 </edam_topics>
13 <edam_operations>
14 <edam_operation>operation_0335</edam_operation> <!-- Formatting -->
15 </edam_operations>
16 <expand macro="requirements">
17 <expand macro="requirement_pigz" />
18 </expand>
19 <expand macro="version_command" />
20
21 <!-- ***************************************************************** -->
22
23 <command detect_errors="aggressive" strict="true">
24 <![CDATA[
25
26 set -o pipefail;
27
28 fq_interleave
29 --1 $input1
30 --2 $input2
31 $check
32 $rename
33 $compress_output
34 > $output
35
36 ]]>
37 </command>
38
39 <!-- ***************************************************************** -->
40
41 <inputs>
42 <param name="input1"
43 type="data"
44 format="fastqsanger,fastq,fastqsanger.gz,fastq.gz"
45 label="Forward reads"
46 help="Forward read FASTQ file" />
47 <param name="input2"
48 type="data"
49 format="fastqsanger,fastq,fastqsanger.gz,fastq.gz"
50 label="Reverse reads"
51 help="Reverse read FASTQ file" />
52 <param argument="--check"
53 type="boolean"
54 label="Check names"
55 checked="False"
56 truevalue="--check"
57 falsevalue=""
58 help="Verify that paired names match" />
59 <param argument="--rename"
60 type="boolean"
61 label="Rename"
62 checked="False"
63 truevalue="--rename"
64 falsevalue=""
65 help="Ensure /1 and /2 at end of read names" />
66 <param name="compress_output"
67 type="boolean"
68 checked="true"
69 truevalue="@PIPE_PIGZ@"
70 falsevalue=""
71 label="Compress output" />
72 </inputs>
73
74 <!-- ***************************************************************** -->
75
76 <outputs>
77 <data name="output" format="fastq.gz">
78 <change_format>
79 <when input="compress_output" value="" format="fastq" />
80 </change_format>
81 </data>
82 </outputs>
83
84 <!-- ***************************************************************** -->
85
86 <tests>
87
88 <!-- default options -->
89 <test expect_num_outputs="1">
90 <param name="input1" value="test_R1.sync.fq" ftype="fastq" />
91 <param name="input2" value="test_R2.sync.fq" ftype="fastq" />
92 <output name="output" file="test.il.fq" compare="diff" ftype="fastq.gz" decompress="true"/>
93 <assert_command>
94 <not_has_text text="--check " />
95 <not_has_text text="--rename " />
96 </assert_command>
97 </test>
98 <!-- mismatched inputs -->
99 <test expect_failure="true">
100 <param name="input1" value="test_R1.fq" ftype="fastq" />
101 <param name="input2" value="test_R2.fq" ftype="fastq" />
102 <param name="check" value="true" />
103 </test>
104 <!-- other options -->
105 <test expect_num_outputs="1">
106 <param name="input1" value="test_R1.sync.fq" ftype="fastq" />
107 <param name="input2" value="test_R2.sync.fq" ftype="fastq" />
108 <param name="check" value="true" />
109 <param name="rename" value="true" />
110 <param name="compress_output" value="false" />
111 <output name="output" file="test.il.fq" compare="diff" ftype="fastq" />
112 <assert_command>
113 <has_text text="--check" />
114 <has_text text="--rename" />
115 </assert_command>
116 </test>
117
118 </tests>
119
120 <!-- ***************************************************************** -->
121
122 <help>
123
124 sync_reads is a utility from b2b-utils for synchronizing a pair of forward and
125 reverse FASTQ read files. It will output a new pair of files containing only
126 read pairs found in both input files. It can optionally output singletons from
127 each input file as well.
128
129 </help>
130
131 <!-- ***************************************************************** -->
132
133 <citations>
134 </citations>
135
136 </tool>
137