Mercurial > repos > jvolkening > b2b_fq_deinterleave

comparison fq_deinterleave.xml @ 0:b42eb9ff6a8c draft

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 00:47:53 +0000
parents
children 3cab918bc851
comparison
equal deleted inserted replaced
-1:000000000000 0:b42eb9ff6a8c
1 <tool id="b2b_@TOOL_NAME@" name="Interleave reads"
2 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT" profile="21.01">
3 <description>Interleaved paired FASTQ files</description>
4 <macros>
5 <token name="@TOOL_NAME@">fq_deinterleave</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="version_command" />
18
19 <!-- ***************************************************************** -->
20
21 <command detect_errors="aggressive">
22 <![CDATA[
23
24 fq_deinterleave
25 --in $input
26 --1 $output1
27 --2 $output2
28 $check
29 $norename
30 $compress_output
31 ## (see e.g. samtools wrappers, which also need to force overwrite)
32 --force
33
34 ]]>
35 </command>
36
37 <!-- ***************************************************************** -->
38
39 <inputs>
40 <param name="input"
41 type="data"
42 format="fastqsanger,fastq,fastqsanger.gz,fastq.gz"
43 label="Interleaved reads"
44 help="FASTQ file" />
45 <param argument="--check"
46 type="boolean"
47 label="Check names"
48 checked="true"
49 truevalue="--check"
50 falsevalue=""
51 help="Verify that paired names match" />
52 <param argument="--norename"
53 type="boolean"
54 label="Don't rename"
55 checked="False"
56 truevalue="--norename"
57 falsevalue=""
58 help="Don't strip /1 and /2 suffixes from end of read names" />
59 <param name="compress_output"
60 type="boolean"
61 checked="true"
62 truevalue="--compress"
63 falsevalue=""
64 label="Compress output" />
65 </inputs>
66
67 <!-- ***************************************************************** -->
68
69 <outputs>
70 <data name="output1" format="fastq.gz" label="${tool.name} on ${on_string} (fwd)">
71 <change_format>
72 <when input="compress_output" value="" format="fastq" />
73 </change_format>
74 </data>
75 <data name="output2" format="fastq.gz" label="${tool.name} on ${on_string} (rev)">
76 <change_format>
77 <when input="compress_output" value="" format="fastq" />
78 </change_format>
79 </data>
80 </outputs>
81
82 <!-- ***************************************************************** -->
83
84 <tests>
85
86 <!-- default options -->
87 <test>
88 <param name="input" value="test.il.fq" />
89 <output name="output1" file="test_R1.rename.fq" compare="diff" ftype="fastq.gz" decompress="true" />
90 <output name="output2" file="test_R2.rename.fq" compare="diff" ftype="fastq.gz" decompress="true" />
91 <assert_command>
92 <not_has_text text="--norename " />
93 </assert_command>
94 </test>
95 <!-- mismatched inputs -->
96 <test expect_failure="true">
97 <param name="input" value="test.il.bad.fq" />
98 <param name="check" value="true" />
99 </test>
100 <!-- other options -->
101 <test expect_num_outputs="2">
102 <param name="input" value="test.il.fq" />
103 <param name="check" value="true" />
104 <param name="norename" value="true" />
105 <param name="compress_output" value="false" />
106 <output name="output1" file="test_R1.sync.fq" compare="diff" ftype="fastq" />
107 <output name="output2" file="test_R2.sync.fq" compare="diff" ftype="fastq" />
108 <assert_command>
109 <has_text text="--check" />
110 <has_text text="--norename" />
111 </assert_command>
112 </test>
113
114 </tests>
115
116 <!-- ***************************************************************** -->
117
118 <help>
119
120 sync_reads is a utility from b2b-utils for synchronizing a pair of forward and
121 reverse FASTQ read files. It will output a new pair of files containing only
122 read pairs found in both input files. It can optionally output singletons from
123 each input file as well.
124
125 </help>
126
127 <!-- ***************************************************************** -->
128
129 <citations>
130 </citations>
131
132 </tool>
133