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comparison nanopore_qc.xml @ 0:e0006d8bf849 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
author jvolkening
date Sat, 02 Mar 2024 03:35:34 +0000
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-1:000000000000 0:e0006d8bf849
1 <tool id="nanopore_qc" name="NanoporeQC" version="0.003">
2
3 <description>Quality report for nanopore data</description>
4
5 <requirements>
6 <requirement type="package" version="3.5.0">r-ggplot2</requirement>
7 <requirement type="package" version="1.1.4">r-dplyr</requirement>
8 <requirement type="package" version="1.3.1">r-tidyr</requirement>
9 <requirement type="package" version="2.1.5">r-readr</requirement>
10 <requirement type="package" version="2.3.8">r-yaml</requirement>
11 <requirement type="package" version="1.3.0">r-scales</requirement>
12 <requirement type="package" version="1.4.3">r-futile.logger</requirement>
13 <requirement type="package" version="1.14.10">r-data.table</requirement>
14 <requirement type="package" version="1.7.4">r-optparse</requirement>
15 <requirement type="package" version="0.88">perl-yaml-libyaml</requirement>
16 </requirements>
17
18 <stdio>
19 <exit_code range="1:" level="fatal" description="Unknown error" />
20 <exit_code range=":-1" level="fatal" description="Unknown error" />
21 </stdio>
22
23 <version_command>
24 <![CDATA[
25 echo '0.003'
26 ]]>
27 </version_command>
28
29 <command>
30 <![CDATA[
31
32 mkdir -p '${html_file.files_path}'
33
34 &&
35
36 Rscript '${__tool_directory__}/nanopore_qc.R'
37 -i '$input'
38 -o '${html_file.files_path}'
39 -q '$q_cutoff'
40 $discard_failed
41
42 &&
43
44 perl '${__tool_directory__}/yaml_to_html.pl'
45
46 '${html_file.files_path}/summary.yaml'
47 '${html_file.files_path}'
48 '$html_file'
49
50 ]]>
51 </command>
52
53 <inputs>
54 <param name="input" type="data" format="tabular" label="Basecall summary file from Albacore"/>
55 <param name="q_cutoff" type="float" value="10" min="0" label="Quality cutoff for QC calculations" />
56 <param name="discard_failed" type="boolean" checked="false" truevalue="--discard_failed T" falsevalue="" label="Ignore reads failing quality filter" />
57 </inputs>
58 <outputs>
59 <data format="html" name="html_file" label="NanoporeQC on ${on_string}" />
60 </outputs>
61 <tests>
62 <!-- binary image blobs can differ, which is why we use line matching
63 instead of file matching -->
64
65 <!-- quality cutoff 10 -->
66 <test>
67 <param name="input" value="sequencing_summary.txt.small" ftype="tabular" />
68 <param name="q_cutoff" value="10" />
69 <output name="html_file">
70 <assert_contents>
71 <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;9990&lt;/td&gt;" />
72 <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;7952&lt;/td&gt;" />
73 </assert_contents>
74 </output>
75 </test>
76
77 <!-- quality cutoff 6 -->
78 <test>
79 <param name="input" value="sequencing_summary.txt.small" ftype="tabular" />
80 <param name="q_cutoff" value="6" />
81 <output name="html_file">
82 <assert_contents>
83 <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;9990&lt;/td&gt;" />
84 <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;9254&lt;/td&gt;" />
85 </assert_contents>
86 </output>
87 </test>
88
89 <!-- quality cutoff 6, discard filtered -->
90 <test>
91 <param name="input" value="sequencing_summary.txt.small" ftype="tabular" />
92 <param name="q_cutoff" value="6" />
93 <param name="discard_failed" value="true" />
94 <output name="html_file">
95 <assert_contents>
96 <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;9107&lt;/td&gt;" />
97 <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;9107&lt;/td&gt;" />
98 </assert_contents>
99 </output>
100 </test>
101
102 <!-- Dorado output -->
103 <test>
104 <param name="input" value="dorado.txt.small" ftype="tabular" />
105 <param name="q_cutoff" value="6" />
106 <output name="html_file">
107 <assert_contents>
108 <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;31&lt;/td&gt;" />
109 <has_text_matching expression="&lt;td&gt;Total Reads&lt;/td&gt;\s*&lt;td&gt;29&lt;/td&gt;" />
110 </assert_contents>
111 </output>
112 </test>
113
114 </tests>
115 <help>
116 <![CDATA[
117 `NanoporeQC` produces a QC report for nanopore sequencing data. It utilizes
118 the summary table produced by Albacore, which saves time by avoiding the
119 need to re-parse the FAST5 read data. `NanoporeQC` was originally forked
120 from the `minion_qc` codebase (https://github.com/roblanf/minion_qc).
121
122 There are only two tuneable parameters. The 'quality cutoff' sets a
123 threshold for plotting: two summaries are produced for each table and plot
124 -- one for all reads (with length >= 0) and one for reads with a quality
125 value greater than the cutoff. 'Ignore reads failing quality filter'
126 indicates whether to include or exclude failing reads from the QC plots.
127 ]]>
128 </help>
129 <citations>
130 <citation type='doi'>10.1093/bioinformatics/bty654</citation>
131 </citations>
132 </tool>