view feature_merge.xml @ 3:fa51a1231daf draft

"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/feature_merge commit 1a4a12b842525e3eeeadba09ef682e17efd65f2c"

<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>