changeset 0:61c4522b2cfe draft

"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/feature_merge commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/feature_merge.xml	Fri Jan 24 17:36:38 2020 -0500
@@ -0,0 +1,68 @@
+<tool id="feature-merge" name="GFF/GTF Feature Merge" version="1.0" profile="16.04">
+    <description>Merge GFF features based on a variety of criteria</description>
+    <requirements>
+        <!--requirement type="package" version="1.0.0">feature_merge</requirement-->
+        <requirement type="package" version="3.7">python</requirement>
+        <requirement type="package" version="1.1">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>