Mercurial > repos > brinkmanlab > feature_merge

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/feature_merge commit afc9f4ade42686dcf53a2615d90e1e9962cf1561"
author brinkmanlab
date Thu, 04 Feb 2021 01:32:31 +0000
parents fefd7cb5d9aa
children
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fa51a1231daf "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/feature_merge commit 1a4a12b842525e3eeeadba09ef682e17efd65f2c"
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1 <tool id="feature-merge" name="GFF/GTF Feature Merge" version="1.3" profile="16.04">
0
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2 <description>Merge GFF features based on a variety of criteria</description>
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3 <requirements>
4
fefd7cb5d9aa "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/feature_merge commit 750b3ad6a19e1bcc7b77b46ad8e2ae6874ab72a4"
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4 <requirement type="package" version="1.3.0">feature_merge</requirement>
0
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5 </requirements>
61c4522b2cfe "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/feature_merge commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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6 <version_command><![CDATA[ feature_merge -v ]]></version_command>
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7 <command detect_errors="aggressive"><![CDATA[
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8 feature_merge $ignore_strand $exclude_components $exact_only -m $merge_strategy
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9 #if $threshold != 0
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10 -t $threshold
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11 #end if
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cc4bffe1d9b5 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/feature_merge commit afc9f4ade42686dcf53a2615d90e1e9962cf1561"
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12 #for $set in $features
0
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13 -f '${str($set.csv).replace(" ", "")}'
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14 #end for
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15 #for $input in $inputs
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16 $input
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17 #end for
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18 > $output
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19 ]]></command>
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20 <inputs>
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21 <param name="inputs" type="data" format="gff,gff3,gtf" multiple="true" label="Input" />
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22 <param name="ignore_strand" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Ignore feature strand when merging" argument="-i"/>
61c4522b2cfe "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/feature_merge commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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23 <param name="exclude_components" type="boolean" checked="false" truevalue="" falsevalue="-e" label="Include original feature records in output" argument="-e"/>
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24 <param name="exact_only" type="boolean" checked="false" truevalue="-x" falsevalue="" label="Only merge features with identical coordinates" argument="-x"/>
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25 <param name="threshold" type="integer" value="0" label="Merge features within a threshold distance from their ends" argument="-t"/>
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26 <param name="merge_strategy" type="select" label="ID conflict resolution strategy" argument="-m">
61c4522b2cfe "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/feature_merge commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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27 <option value="merge">merge: attributes of all features with the same primary key will be merged</option>
61c4522b2cfe "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/feature_merge commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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28 <option value="append" selected="true">append: entry will have a unique, autoincremented primary key assigned to it</option>
61c4522b2cfe "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/feature_merge commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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29 <option value="error">error: exception will be raised. This means you will have to edit the file yourself to fix the duplicated IDs</option>
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30 <option value="skip">skip: ignore duplicates, emitting a warning</option>
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31 <option value="replace">replace: keep last duplicate</option>
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32 </param>
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33 <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.">
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34 <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"/>
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35 </repeat>
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36 </inputs>
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37 <outputs>
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38 <data name="output" format="gff" />
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39 </outputs>
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40 <tests>
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41 <test expect_num_outputs="1">
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42 <param name="inputs" >
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43 <collection type="list">
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44 <element name="test1" value="feature_merge/test-data/615598_genome.gbk_2.gff3" ftype="gff3" />
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45 <element name="test2" value="feature_merge/test-data/915596_genome.gbk_2.gff3" ftype="gff3" />
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46 <element name="test3" value="feature_merge/test-data/615598_genome.gbk_1.gff3" ftype="gff3" />
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47 <element name="test4" value="feature_merge/test-data/1015597_genome.gbk_2.gff3" ftype="gff3" />
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48 <element name="test5" value="feature_merge/test-data/915596_genome.gbk_1.gff3" ftype="gff3" />
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49 <element name="test6" value="feature_merge/test-data/1015597_genome.gbk_1.gff3" ftype="gff3" />
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50 </collection>
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51 </param>
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52 <param name="ignore_strand" value="-i" />
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53 <output name="output" file="test-data/output.gff3" ftype="gff3" />
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54 </test>
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55 </tests>
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56 <help><![CDATA[
61c4522b2cfe "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/feature_merge commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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57 GFF/GTF Feature Merge
61c4522b2cfe "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/feature_merge commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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58 Merge GFF features based on a variety of criteria.
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59
61c4522b2cfe "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/feature_merge commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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60 https://github.com/brinkmanlab/feature_merge
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61 ]]></help>
61c4522b2cfe "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/feature_merge commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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62 <citations>
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63 <citation type="doi">10.5281/zenodo.3364784</citation>
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64 <citation type="doi">10.5281/zenodo.3364789</citation>
61c4522b2cfe "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/feature_merge commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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65 </citations>
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66 </tool>