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comparison brew3r_r.xml @ 0:928a52b5c938 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
author iuc
date Tue, 11 Jun 2024 08:26:37 +0000
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-1:000000000000 0:928a52b5c938
1 <tool id="brew3r_r" name="BREW3R.r" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
2 <description>Extend GTF</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.0.1</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
7 <edam_topics>
8 <edam_topic>topic_3308</edam_topic>
9 </edam_topics>
10 <edam_operations>
11 <edam_operation>operation_0362</edam_operation>
12 </edam_operations>
13 <xrefs>
14 <!-- <xref type="bio.tools">BREW3R.r</xref> -->
15 <xref type="bioconductor">BREW3R.r</xref>
16 </xrefs>
17 <requirements>
18 <!-- <requirement type="package" version="@TOOL_VERSION@">bioconductor-brew3r.r</requirement>
19 <requirement type="package" version="1.64.0">bioconductor-rtracklayer</requirement>
20 <requirement type="package" version="1.20.4">r-getopt</requirement> -->
21 <container type="docker">lldelisle/brew3r:v2</container>
22 </requirements>
23 <required_files>
24 <include path="brew3r.r_script.R" />
25 </required_files>
26 <version_command><![CDATA[
27 echo $(R --version | grep version | grep -v GNU)", BREW3R.r version" $(R --vanilla --slave -e "library(BREW3R.r); cat(sessionInfo()\$otherPkgs\$BREW3R.r\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
28 ]]></version_command>
29 <command detect_errors="exit_code"><![CDATA[
30 Rscript '${__tool_directory__}/brew3r.r_script.R'
31 --gtf_to_extend '$gtf_to_extend'
32 --gtf_to_overlap '$gtf_to_overlap'
33 #if '$sup_output' == 'true':
34 --sup_output '$output_table'
35 #end if
36 #if str($no_add) != '':
37 '$no_add'
38 #end if
39 #if str($exclude_pattern) != '':
40 --exclude_pattern '$exclude_pattern'
41 #end if
42 #if str($filter_unstranded) != '':
43 '$filter_unstranded'
44 #end if
45 -o output.gtf
46
47 ]]></command>
48 <inputs>
49 <param argument="--gtf_to_extend" type="data" format="gtf" label="Input gtf file to be extended on 3'" help="Usually coming from public resource." />
50 <param argument="--gtf_to_overlap" type="data" format="gtf" label="Input gtf file that will be used to extend" help="Coming from StringTie or another public resource." />
51 <param argument="--sup_output" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Get a supplementary output table with resolution of overlaps" />
52 <param argument="--no_add" type="boolean" truevalue="--no_add" falsevalue="" checked="false" label="Do not add new exons" />
53 <param argument="--exclude_pattern" type="text" value="" label="Do not extend genes with names matching this pattern" help="Leave empty if you want to extend all genes.">
54 <sanitizer>
55 <valid initial="string.printable">
56 <remove value="'"/>
57 <remove value="\"/>
58 </valid>
59 </sanitizer>
60 </param>
61 <param argument="--filter_unstranded" type="boolean" truevalue="--filter_unstranded" falsevalue="" checked="false" label="Filter unstranded intervals that overlaps genes of both strands" help="Recommanded if you used StringTie on unstranded libraries." />
62 </inputs>
63 <outputs>
64 <data name="output" format="gtf" from_work_dir="output.gtf" label="${tool.name} on ${gtf_to_extend.name} and ${gtf_to_overlap.name}: GTF" />
65 <data name="output_table" format="tabular" label="${tool.name} on ${gtf_to_extend.name} and ${gtf_to_overlap.name}: overlap resolution">
66 <filter>sup_output == True</filter>
67 </data>
68 </outputs>
69 <tests>
70 <test expect_num_outputs="1">
71 <param name="gtf_to_extend" value="input.gtf"/>
72 <param name="gtf_to_overlap" value="second_input.gtf"/>
73 <output name="output" value="output.gtf" compare="diff" lines_diff="2"/>
74 </test>
75 <test expect_num_outputs="1">
76 <param name="gtf_to_extend" value="input.gtf"/>
77 <param name="gtf_to_overlap" value="second_input.gtf"/>
78 <param name="no_add" value="true"/>
79 <output name="output">
80 <assert_contents>
81 <has_n_lines n="31"/>
82 <not_has_text text="BREW3R"/>
83 </assert_contents>
84 </output>
85 </test>
86 <test expect_num_outputs="1">
87 <param name="gtf_to_extend" value="input.gtf"/>
88 <param name="gtf_to_overlap" value="second_input.gtf"/>
89 <param name="exclude_pattern" value="^Gm"/>
90 <output name="output">
91 <assert_contents>
92 <has_n_lines n="34"/>
93 <not_has_text text="exon111.ext"/>
94 </assert_contents>
95 </output>
96 </test>
97 <test expect_num_outputs="1">
98 <param name="gtf_to_extend" value="input.gtf"/>
99 <param name="gtf_to_overlap" value="second_input.gtf"/>
100 <param name="exclude_pattern" value="Gm$"/>
101 <output name="output" value="output.gtf" compare="diff" lines_diff="2"/>
102 <assert_command>
103 <has_text text="--exclude_pattern 'Gm$'"/>
104 </assert_command>
105 </test>
106 <test expect_num_outputs="1">
107 <param name="gtf_to_extend" value="input.gtf"/>
108 <param name="gtf_to_overlap" value="second_input.gtf"/>
109 <param name="filter_unstranded" value="true"/>
110 <output name="output">
111 <assert_contents>
112 <has_n_lines n="36"/>
113 <not_has_text text="exon121.ext"/>
114 </assert_contents>
115 </output>
116 </test>
117 </tests>
118 <help><![CDATA[
119
120 .. class:: infomark
121
122 **What it does**
123
124 This tool extend the annotations existing in an input GTF file in the 3' end using annotations from another input GTF. During the process, it makes sure that there will not be new overlaps between different genes.
125
126 Usage
127 .....
128
129
130 **Input**
131
132 2 GTF files:
133 - First one to extend usually comes from a public resource.
134 - Second one that is used as template may come from a public resource or from StringTie.
135
136
137 **Output**
138
139 1 GTF file with all exons from the input GTF where some of them have been extended (the exon_id ends with '.ext') and potentially new exons (the exon_id contains BREW3R).
140
141 ]]></help>
142 <citations>
143 <citation type="bibtex">
144 @unpublished{None,
145 author = {Lucille Lopez-Delisle},
146 title = {None},
147 year = {None},
148 eprint = {None},
149 url = {https://github.com/lldelisle/BREW3R.r}
150 }</citation>
151 </citations>
152 </tool>