Mercurial > repos > nml > quasitools
comparison quality.xml @ 5:b69e898b8109 draft
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
author | nml |
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date | Fri, 24 Aug 2018 16:50:28 -0400 |
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children | dcd43b402eb3 |
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4:8cdffc02d2e2 | 5:b69e898b8109 |
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1 <tool id="quality" name="Quality control" version="0.4.2"> | |
2 <description>Performs quality control on FASTQ reads.</description> | |
3 <requirements> | |
4 <requirement type="package" version="0.4.2">quasitools</requirement> | |
5 </requirements> | |
6 <command detect_errors="exit_code"><![CDATA[ | |
7 | |
8 quasitools quality | |
9 | |
10 ## Preparing file input. | |
11 #if $data_type.type == "paired": | |
12 | |
13 '$data_type.fastq_input1' | |
14 '$data_type.fastq_input2' | |
15 | |
16 #elif $data_type.type == "collection": | |
17 | |
18 '$data_type.fastq_input1.forward' | |
19 '$data_type.fastq_input1.reverse' | |
20 | |
21 #elif $data_type.type == "single": | |
22 | |
23 '$data_type.fastq_input1' | |
24 | |
25 #end if | |
26 | |
27 #if $length_cutoff: | |
28 -lc '$length_cutoff' | |
29 #end if | |
30 | |
31 #if $score_cutoff: | |
32 -sc '$score_cutoff' | |
33 #end if | |
34 | |
35 #if $min_read_qual: | |
36 -rq '$min_read_qual' | |
37 #end if | |
38 | |
39 #if $low_quality.qual_selector == "filter_ns": | |
40 --ns | |
41 #elif $low_quality.qual_selector == "mask_reads": | |
42 --mask_reads | |
43 #end if | |
44 | |
45 #if $score_type.score_selector == "median": | |
46 --median | |
47 #elif $score_type.score_selector == "mean": | |
48 --mean | |
49 #end if | |
50 | |
51 $trim_reads | |
52 | |
53 -o output | |
54 | |
55 ]]></command> | |
56 <inputs> | |
57 <conditional name="data_type"> | |
58 <param name="type" type="select" label="Specify the read type."> | |
59 <option value="single">Single-end Data</option> | |
60 <option value="paired">Paired-end Data</option> | |
61 <option value="collection">Collection Paired-end Data</option> | |
62 </param> | |
63 <when value="single"> | |
64 <param name="fastq_input1" type="data" format="fastq" label="Single end read file(s)"/> | |
65 </when> | |
66 <when value="paired"> | |
67 <param name="fastq_input1" type="data" format="fastq" label="Forward paired-end read file"/> | |
68 <param name="fastq_input2" type="data" format="fastq" label="Reverse paired-end read file"/> | |
69 </when> | |
70 <when value="collection"> | |
71 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastq" collection_type="paired" /> | |
72 </when> | |
73 </conditional> | |
74 <param name="length_cutoff" type="integer" optional="true" min="1" max="1000" label="Length cutoff" value="100" help="Reads which fall short of the specified length will be filtered out. Defaults to 100." /> | |
75 <param name="score_cutoff" type="integer" optional="true" min="0" max="40" label="Score cutoff" value="30" help="Reads whose median or mean quality score (depending on the score type specified) is less than the specified score cutoff value will be filtered out. Defaults to 30." /> | |
76 <param name="min_read_qual" type="integer" optional="true" min="1" max="100" label="Minimum quality" value="30" help="Minimum required quality for a position in a read not to be masked, is masking is enabled. Defaults to 30." /> | |
77 <param name="trim_reads" type="boolean" optional="true" checked="false" truevalue="-tr" falsevalue="" label="Trim reads" help="Iteratively trim reads based on filter values if enabled." /> | |
78 <conditional name="low_quality"> | |
79 <param name="qual_selector" type="select" label="Filter out regions masked, or mask low coverage regions with n's." multiple="false" display="radio"> | |
80 <option value="filter_ns">Filter out regions with n's</option> | |
81 <option value="mask_reads">Mask low coverage regions with n's</option> | |
82 <option value="neither" selected="true">Do not filter or mask low coverage regions.</option> | |
83 </param> | |
84 <when value="filter_ns"> | |
85 </when> | |
86 <when value="mask_reads"> | |
87 </when> | |
88 <when value="neither"> | |
89 </when> | |
90 </conditional> | |
91 <conditional name="score_type"> | |
92 <param name="score_selector" type="select" label="Use either median score (default) or mean score for the score cutoff value." multiple="false" display="radio"> | |
93 <option value="median" selected="true">Use median score</option> | |
94 <option value="mean">Use mean score</option> | |
95 </param> | |
96 <when value="median"> | |
97 </when> | |
98 <when value="mean"> | |
99 </when> | |
100 </conditional> | |
101 </inputs> | |
102 <outputs> | |
103 <data format="fastq" label="Quality control output" name="output_filtered" from_work_dir="output/filtered.fastq" /> | |
104 </outputs> | |
105 <tests> | |
106 <test> | |
107 <param name="type" value="single"/> | |
108 <param name="fastq_input1" value="forward.fastq" /> | |
109 <param name="score_selector" value="median" /> | |
110 <output name="output_filtered"> | |
111 <assert_contents> | |
112 <has_text text="@M01647:10:000000000-ACPHB:1:1101:18589:1580 1:N:0:86" /> | |
113 <has_text text="CCCCCGG@FFGGGGGGGGGGGGCGGGGGGGGDGFFFGGGGGDEGCFGCFFFGGGGGGGGGGGGGGGGFGGGGGGGGGGFCFCGGGGCGFGGGGFGEGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGF" /> | |
114 </assert_contents> | |
115 </output> | |
116 </test> | |
117 <test> | |
118 <param name="type" value="single"/> | |
119 <param name="fastq_input1" value="forward.fastq" /> | |
120 <param name="score_selector" value="median" /> | |
121 <param name="qual_selector" value="filter_ns" /> | |
122 <output name="output_filtered"> | |
123 <assert_contents> | |
124 <has_text text="@M01647:10:000000000-ACPHB:1:1101:18589:1580 1:N:0:86" /> | |
125 <has_text text="CCCCCGG@FFGGGGGGGGGGGGCGGGGGGGGDGFFFGGGGGDEGCFGCFFFGGGGGGGGGGGGGGGGFGGGGGGGGGGFCFCGGGGCGFGGGGFGEGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGF" /> | |
126 </assert_contents> | |
127 </output> | |
128 </test> | |
129 <test> | |
130 <param name="type" value="single"/> | |
131 <param name="fastq_input1" value="forward.fastq" /> | |
132 <param name="score_selector" value="median" /> | |
133 <param name="trim_reads" value="-tr" /> | |
134 <output name="output_filtered"> | |
135 <assert_contents> | |
136 <has_text text="@M01647:10:000000000-ACPHB:1:1101:18589:1580 1:N:0:86" /> | |
137 <has_text text="CCCCCGG@FFGGGGGGGGGGGGCGGGGGGGGDGFFFGGGGGDEGCFGCFFFGGGGGGGGGGGGGGGGFGGGGGGGGGGFCFCGGGGCGFGGGGFGEGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGF" /> | |
138 </assert_contents> | |
139 </output> | |
140 </test> | |
141 <test> | |
142 <param name="type" value="single"/> | |
143 <param name="fastq_input1" value="forward.fastq" /> | |
144 <param name="score_selector" value="median" /> | |
145 <param name="qual_selector" value="mask_reads" /> | |
146 <output name="output_filtered"> | |
147 <assert_contents> | |
148 <has_text text="@M01647:10:000000000-ACPHB:1:1101:18589:1580 1:N:0:86" /> | |
149 <has_text text="NNNNNNTACCACATCCCNCNNNNTTNNNNNNNNNNANNTCNNTNNCNNTNCTNNNTNTNNNTGNTGCNTNTTTTTCAGTTCCCTTNGNTGNNGNCTTCAGNNNNTATACTGCATTTACCNTNCNT" /> | |
150 </assert_contents> | |
151 </output> | |
152 </test> | |
153 <test> | |
154 <param name="type" value="single"/> | |
155 <param name="fastq_input1" value="forward.fastq" /> | |
156 <param name="score_selector" value="mean" /> | |
157 <output name="output_filtered"> | |
158 <assert_contents> | |
159 <has_text text="@M01647:10:000000000-ACPHB:1:1101:10485:1674 1:N:0:86" /> | |
160 <has_text text="CCCCCGG@FFGGGGGGGGGGGGCGGGGGGGGDGFFFGGGGGDEGCFGCFFFGGGGGGGGGGGGGGGGFGGGGGGGGGGFCFCGGGGCGFGGGGFGEGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGF" /> | |
161 </assert_contents> | |
162 </output> | |
163 </test> | |
164 </tests> | |
165 <help><![CDATA[ | |
166 Quality Control | |
167 =============== | |
168 | |
169 Perform quality control on FASTQ reads.]]></help> | |
170 <citations> | |
171 </citations> | |
172 </tool> |