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comparison feature_merge.xml @ 0:61c4522b2cfe draft

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/feature_merge commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
author brinkmanlab
date Fri, 24 Jan 2020 17:36:38 -0500
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-1:000000000000 0:61c4522b2cfe
1 <tool id="feature-merge" name="GFF/GTF Feature Merge" version="1.0" profile="16.04">
2 <description>Merge GFF features based on a variety of criteria</description>
3 <requirements>
4 <!--requirement type="package" version="1.0.0">feature_merge</requirement-->
5 <requirement type="package" version="3.7">python</requirement>
6 <requirement type="package" version="1.1">feature_merge</requirement>
7 </requirements>
8 <version_command><![CDATA[ feature_merge -v ]]></version_command>
9 <command detect_errors="aggressive"><![CDATA[
10 feature_merge $ignore_strand $exclude_components $exact_only -m $merge_strategy
11 #if $threshold != 0
12 -t $threshold
13 #end if
14 #for set in $features
15 -f '${str($set.csv).replace(" ", "")}'
16 #end for
17 #for $input in $inputs
18 $input
19 #end for
20 > $output
21 ]]></command>
22 <inputs>
23 <param name="inputs" type="data" format="gff,gff3,gtf" multiple="true" label="Input" />
24 <param name="ignore_strand" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Ignore feature strand when merging" argument="-i"/>
25 <param name="exclude_components" type="boolean" checked="false" truevalue="" falsevalue="-e" label="Include original feature records in output" argument="-e"/>
26 <param name="exact_only" type="boolean" checked="false" truevalue="-x" falsevalue="" label="Only merge features with identical coordinates" argument="-x"/>
27 <param name="threshold" type="integer" value="0" label="Merge features within a threshold distance from their ends" argument="-t"/>
28 <param name="merge_strategy" type="select" label="ID conflict resolution strategy" argument="-m">
29 <option value="merge">merge: attributes of all features with the same primary key will be merged</option>
30 <option value="append" selected="true">append: entry will have a unique, autoincremented primary key assigned to it</option>
31 <option value="error">error: exception will be raised. This means you will have to edit the file yourself to fix the duplicated IDs</option>
32 <option value="skip">skip: ignore duplicates, emitting a warning</option>
33 <option value="replace">replace: keep last duplicate</option>
34 </param>
35 <repeat name="features" title="Specify features to merge" help="Can be provided more than once to specify multiple merge groups. If not provided, all features will be merged.">
36 <param name="csv" type="text" label="Feature set to merge" help="Comma seperated types of features to merge. Must be terms or accessions from the SOFA sequence ontology, ALL, or NONE" argument="-f"/>
37 </repeat>
38 </inputs>
39 <outputs>
40 <data name="output" format="gff" />
41 </outputs>
42 <tests>
43 <test expect_num_outputs="1">
44 <param name="inputs" >
45 <collection type="list">
46 <element name="test1" value="feature_merge/test-data/615598_genome.gbk_2.gff3" ftype="gff3" />
47 <element name="test2" value="feature_merge/test-data/915596_genome.gbk_2.gff3" ftype="gff3" />
48 <element name="test3" value="feature_merge/test-data/615598_genome.gbk_1.gff3" ftype="gff3" />
49 <element name="test4" value="feature_merge/test-data/1015597_genome.gbk_2.gff3" ftype="gff3" />
50 <element name="test5" value="feature_merge/test-data/915596_genome.gbk_1.gff3" ftype="gff3" />
51 <element name="test6" value="feature_merge/test-data/1015597_genome.gbk_1.gff3" ftype="gff3" />
52 </collection>
53 </param>
54 <param name="ignore_strand" value="-i" />
55 <output name="output" file="test-data/output.gff3" ftype="gff3" />
56 </test>
57 </tests>
58 <help><![CDATA[
59 GFF/GTF Feature Merge
60 Merge GFF features based on a variety of criteria.
61
62 https://github.com/brinkmanlab/feature_merge
63 ]]></help>
64 <citations>
65 <citation type="doi">10.5281/zenodo.3364784</citation>
66 <citation type="doi">10.5281/zenodo.3364789</citation>
67 </citations>
68 </tool>