Mercurial > repos > lldelisle > fromgtftobed12

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planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 commit 15b8c2cc83708044413a152322bcbfca8a74d29a
author lldelisle
date Fri, 03 Nov 2023 14:13:51 +0000
parents 418e4d0fe0bd
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1 <tool id="fromgtfTobed12" name="fromgtftobed12" version="0.11.1+galaxy1">
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2 <description> Convert a gtf to a bed12.</description>
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3 <requirements>
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4 <requirement type="package" version="0.11.1">gffutils</requirement>
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5 </requirements>
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6 <stdio>
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7 <!-- Anything other than zero is an error -->
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8 <exit_code range="1:" />
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9 <exit_code range=":-1" />
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10 <!-- In case the return code has not been set propery check stderr too -->
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11 <regex match="Error:" />
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12 <regex match="Exception:" />
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13 </stdio>
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14 <command>
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15 <![CDATA[
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16 python3 $__tool_directory__/fromgtfTobed12.py
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17 #if str($preferedName) != "":
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18 --preferedName $preferedName
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19 #end if
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20 $mergeTranscripts
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21 $ucscformat
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22 --output $output
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23 $input
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24 ]]>
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25 </command>
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26 <inputs>
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27 <param name="input" multiple="false" type="data" format="gtf" label="Select the gtf to convert."/>
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28 <param name="mergeTranscripts" type="select" label="Do you want to merge all transcripts of a gene in a single line?">
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29 <option value="" selected="true">No</option>
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30 <option value="--mergeTranscripts">Yes</option>
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31 <option value="--mergeTranscriptsAndOverlappingExons">Yes and merge overlapping exons</option>
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32 </param>
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33 <param argument="--preferedName" type="text" value="" label="Use a specific name for the 4th column" help="By default the 4th column will be transcript_name or gene_name if you merge transcripts. If you prefer 'gene_id', for example, then set this option." />
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34 <param argument="--ucscformat" type="boolean" checked="True" truevalue="--ucscformat" falsevalue="" label="If you want that all chromosome names begin with 'chr'."/>
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35 </inputs>
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36
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37 <outputs>
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38 <data format="bed" name="output" label="$input.name as bed12"/>
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39 </outputs>
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40
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41 <tests>
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42 <test>
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43 <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/>
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44 <param name="ucscformat" value="--ucscformat"/>
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45 <output name="output" file="test.bed"/>
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46 </test>
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47 <test>
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48 <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/>
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49 <param name="ucscformat" value="--ucscformat"/>
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50 <param name="preferedName" value="gene_name"/>
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51 <output name="output" file="testWithGenes.bed"/>
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52 </test>
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53 <test>
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54 <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/>
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55 <param name="ucscformat" value="--ucscformat"/>
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56 <param name="preferedName" value="gene_id"/>
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57 <output name="output" file="testWithGeneIds.bed"/>
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58 </test>
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59 <test>
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60 <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/>
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61 <param name="mergeTranscripts" value="--mergeTranscripts"/>
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62 <param name="ucscformat" value=""/>
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63 <output name="output" file="testMergeNotUCSC.bed"/>
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64 </test>
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65 <test>
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66 <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/>
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67 <param name="mergeTranscripts" value="--mergeTranscriptsAndOverlappingExons"/>
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68 <param name="ucscformat" value=""/>
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69 <output name="output" file="testMergeExons.bed"/>
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70 </test>
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71 </tests>
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72 <help><![CDATA[
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73 This tool uses gffutils to convert gtf to bed12. One line per transcript.
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74 It will use as names transcript_name or gene_name when available.
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75 ]]> </help>
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76 <citations>
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77 <citation type="bibtex">@online{gffutils,
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78 url = {https://pythonhosted.org/gffutils/contents.html}
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79 }
418e4d0fe0bd planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 commit 1aaffda5b95e0389e315179345642c0d005867c1
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80 </citation>
418e4d0fe0bd planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 commit 1aaffda5b95e0389e315179345642c0d005867c1
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81 </citations>
418e4d0fe0bd planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 commit 1aaffda5b95e0389e315179345642c0d005867c1
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82 </tool>