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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
author bgruening
date Sun, 12 Sep 2021 19:28:19 +0000
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-1:000000000000 0:7a821cd57b43
1 <tool id="fastq_info" name="FASTQ info" version="@TOOL_VERSION@+Galaxy@SUFFIX_VERSION@" profile="20.01">
2 <description>validates single or paired fastq files</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="edam_ontology"/>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 fastq_info
10 #if $input_option.input_type == 'single'
11 $input_option.fastq_1
12 #else
13 $input_option.fastq_1
14 $input_option.fastq_2
15 #end if
16 $r
17 $q
18 2>&1 | tee ./output.txt
19 ]]> </command>
20 <inputs>
21 <conditional name="input_option">
22 <param name="input_type" type="select" label="Single reads or paired reads" help="Select between paired and single end data">
23 <option value="single">Single</option>
24 <option value="paired">Paired</option>
25 </param>
26 <when value="single">
27 <param name="fastq_1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="FASTQ file" help="Input FASTQ file"/>
28 </when>
29 <when value="paired">
30 <param name="fastq_1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="FASTQ file: forward reads"/>
31 <param name="fastq_2" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="FASTQ file: reverse reads"/>
32 </when>
33 </conditional>
34 <param argument="-q" type="boolean" truevalue="" falsevalue="-q" checked="True" label="Determine quality scoring" help="If this option is disabled, it won't fail if the quality encoding cannot be determined" />
35 <param argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Skip check for duplicated readnames" help="By using this option no checks are made to determine if the read names/identifiers are unique (it will run faster and use less memory)" />
36 </inputs>
37 <outputs>
38 <data name="output" format="txt" from_work_dir="./output.txt" label="${tool.name} on ${on_string}: Validation result">
39 </data>
40 </outputs>
41 <tests>
42 <test expect_num_outputs="1">
43 <conditional name="input_option">
44 <param name="input_type" value="single"/>
45 <param name="fastq_1" value="R1.fastq"/>
46 </conditional>
47 <output name="output" file="output.txt" ftype="txt" lines_diff="2">
48 <assert_contents>
49 <has_text text="OK"/>
50 <has_size value="362" delta="100"/>
51 </assert_contents>
52 </output>
53 </test>
54 <!--Test gzip files-->
55 <test expect_num_outputs="1">
56 <conditional name="input_option">
57 <param name="input_type" value="single"/>
58 <param name="fastq_1" value="R1.fastq.gz"/>
59 </conditional>
60 <output name="output" ftype="txt">
61 <assert_contents>
62 <has_text text="OK"/>
63 <has_size value="368" delta="100"/>
64 </assert_contents>
65 </output>
66 </test>
67 <!--Test paired reads-->
68 <test expect_num_outputs="1">
69 <conditional name="input_option">
70 <param name="input_type" value="paired"/>
71 <param name="fastq_1" value="R1.fastq"/>
72 <param name="fastq_2" value="R2.fastq"/>
73 </conditional>
74 <output name="output">
75 <assert_contents>
76 <has_text text="OK"/>
77 <has_size value="544" delta="100"/>
78 </assert_contents>
79 </output>
80 </test>
81 <!-- Test q option-->
82 <test expect_num_outputs="1">
83 <param name="q" value="False"/>
84 <conditional name="input_option">
85 <param name="input_type" value="single"/>
86 <param name="fastq_1" value="R1.fastq"/>
87 </conditional>
88 <output name="output">
89 <assert_contents>
90 <has_text text="OK"/>
91 <has_size value="362" delta="100"/>
92 </assert_contents>
93 </output>
94 </test>
95 <!-- Test duplicated id -->
96 <test expect_num_outputs="1">
97 <conditional name="input_option">
98 <param name="input_type" value="single"/>
99 <param name="fastq_1" value="R1_duplicated.fastq"/>
100 </conditional>
101 <output name="output">
102 <assert_contents>
103 <has_text text="line 36: duplicated sequence SRR1294492.1207358/1"/>
104 <has_size value="311" delta="100"/>
105 </assert_contents>
106 </output>
107 </test>
108 <!-- Test r option-->
109 <test expect_num_outputs="1">
110 <param name="r" value="True"/>
111 <conditional name="input_option">
112 <param name="input_type" value="single"/>
113 <param name="fastq_1" value="R1_duplicated.fastq"/>
114 </conditional>
115 <output name="output">
116 <assert_contents>
117 <has_text text="OK"/>
118 <has_size value="193" delta="100"/>
119 </assert_contents>
120 </output>
121 </test>
122 <!-- Test truncated file 01 -->
123 <test expect_num_outputs="1">
124 <conditional name="input_option">
125 <param name="input_type" value="paired"/>
126 <param name="fastq_1" value="R1_truncated.fastq"/>
127 <param name="fastq_2" value="R2.fastq"/>
128 </conditional>
129 <output name="output">
130 <assert_contents>
131 <has_text text="line 32: file truncated"/>
132 <has_size value="285" delta="100"/>
133 </assert_contents>
134 </output>
135 </test>
136 <!-- Test truncated file 02 -->
137 <test expect_num_outputs="1">
138 <conditional name="input_option">
139 <param name="input_type" value="paired"/>
140 <param name="fastq_1" value="R1_truncated_entry.fastq"/>
141 <param name="fastq_2" value="R2.fastq"/>
142 </conditional>
143 <output name="output">
144 <assert_contents>
145 <has_text text="unpaired read - SRR1294492.2047212/"/>
146 <has_size value="557" delta="100"/>
147 </assert_contents>
148 </output>
149 </test>
150 </tests>
151 <help><![CDATA[
152 .. class:: infomark
153
154 **Purpose**
155
156 FASTQ info is part of `FASTQ utils <https://github.com/nunofonseca/fastq_utils>`_, a set of Linux utilities to validate and manipulate fastq files.
157
158 ]]> </help>
159 <expand macro="citations"/>
160 </tool>