Mercurial > repos > brinkmanlab > feature_merge
view feature_merge.xml @ 3:fa51a1231daf draft
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/feature_merge commit 1a4a12b842525e3eeeadba09ef682e17efd65f2c"
author | brinkmanlab |
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date | Tue, 12 Jan 2021 21:17:20 +0000 |
parents | fd6ec1fe399b |
children | fefd7cb5d9aa |
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<tool id="feature-merge" name="GFF/GTF Feature Merge" version="1.3" profile="16.04"> <description>Merge GFF features based on a variety of criteria</description> <requirements> <requirement type="package" version="1.3">feature_merge</requirement> </requirements> <version_command><![CDATA[ feature_merge -v ]]></version_command> <command detect_errors="aggressive"><![CDATA[ feature_merge $ignore_strand $exclude_components $exact_only -m $merge_strategy #if $threshold != 0 -t $threshold #end if #for set in $features -f '${str($set.csv).replace(" ", "")}' #end for #for $input in $inputs $input #end for > $output ]]></command> <inputs> <param name="inputs" type="data" format="gff,gff3,gtf" multiple="true" label="Input" /> <param name="ignore_strand" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Ignore feature strand when merging" argument="-i"/> <param name="exclude_components" type="boolean" checked="false" truevalue="" falsevalue="-e" label="Include original feature records in output" argument="-e"/> <param name="exact_only" type="boolean" checked="false" truevalue="-x" falsevalue="" label="Only merge features with identical coordinates" argument="-x"/> <param name="threshold" type="integer" value="0" label="Merge features within a threshold distance from their ends" argument="-t"/> <param name="merge_strategy" type="select" label="ID conflict resolution strategy" argument="-m"> <option value="merge">merge: attributes of all features with the same primary key will be merged</option> <option value="append" selected="true">append: entry will have a unique, autoincremented primary key assigned to it</option> <option value="error">error: exception will be raised. This means you will have to edit the file yourself to fix the duplicated IDs</option> <option value="skip">skip: ignore duplicates, emitting a warning</option> <option value="replace">replace: keep last duplicate</option> </param> <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."> <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"/> </repeat> </inputs> <outputs> <data name="output" format="gff" /> </outputs> <tests> <test expect_num_outputs="1"> <param name="inputs" > <collection type="list"> <element name="test1" value="feature_merge/test-data/615598_genome.gbk_2.gff3" ftype="gff3" /> <element name="test2" value="feature_merge/test-data/915596_genome.gbk_2.gff3" ftype="gff3" /> <element name="test3" value="feature_merge/test-data/615598_genome.gbk_1.gff3" ftype="gff3" /> <element name="test4" value="feature_merge/test-data/1015597_genome.gbk_2.gff3" ftype="gff3" /> <element name="test5" value="feature_merge/test-data/915596_genome.gbk_1.gff3" ftype="gff3" /> <element name="test6" value="feature_merge/test-data/1015597_genome.gbk_1.gff3" ftype="gff3" /> </collection> </param> <param name="ignore_strand" value="-i" /> <output name="output" file="test-data/output.gff3" ftype="gff3" /> </test> </tests> <help><![CDATA[ GFF/GTF Feature Merge Merge GFF features based on a variety of criteria. https://github.com/brinkmanlab/feature_merge ]]></help> <citations> <citation type="doi">10.5281/zenodo.3364784</citation> <citation type="doi">10.5281/zenodo.3364789</citation> </citations> </tool>