Mercurial > repos > iuc > sansa_annotate

annotate macros.xml @ 5:9dee066f5075 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa commit 73ffea5a841e0b6b71c1111f36fee9489c239f2d
author iuc
date Mon, 20 Oct 2025 16:55:59 +0000
parents 88d375af6c46
children
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608c3eefface "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
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1 <?xml version="1.0"?>
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2 <macros>
5
9dee066f5075 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa commit 73ffea5a841e0b6b71c1111f36fee9489c239f2d
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3 <token name="@TOOL_VERSION@">0.2.5</token>
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4 <token name="@VERSION_SUFFIX@">0</token>
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5 <xml name="edam_topics">
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6 <edam_topics>
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7 <edam_topic>topic_3175</edam_topic>
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8 </edam_topics>
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9 </xml>
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10 <xml name="edam_operations">
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11 <edam_operations>
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12 <edam_operation>operation_3197</edam_operation>
b4b8e88c6ff9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit ca0c5ca081608b464ee2698a99b3c5ba31eb58b2"
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13 </edam_operations>
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14 </xml>
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15 <xml name="requirements">
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16 <requirements>
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17 <requirement type="package" version="@TOOL_VERSION@">sansa</requirement>
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18 </requirements>
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19 </xml>
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20 <xml name="version_command">
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21 <version_command><![CDATA[sansa -v | grep "Sansa " | cut -d "v" -f 3]]></version_command>
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22 </xml>
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23 <xml name="citations">
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24 <citations>
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25 <citation type="doi">10.1093/bioinformatics/bts378</citation>
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26 </citations>
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27 </xml>
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28
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29 <!-- input -->
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30
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31 <xml name="fg">
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32 <section name="fg" title="Feature and gene annotation options" expanded="true">
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33 <param argument="--gtf" type="data" format="gtf,gff3" label="Select file"/>
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34 <param argument="--id" type="text" value="gene_name" label="Set GTF/GFF3 attribute">
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35 <option value="exon_id">exon_id</option>
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36 <option value="gene_id">gene_id</option>
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37 <option value="gene_name">gene_name</option>
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38 <option value="Name">Name</option>
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39 </param>
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40 <param argument="--feature" type="text" value="gene" label="Set GTF/GFF3 feature">
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41 <option value="gene">gene</option>
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42 <option value="exon">exon</option>
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43 </param>
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44 <param argument="--distance" type="integer" min="0" value="1000" label="Set maximum distance" help="0: overlapping features only"/>
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45 <param argument="--contained" type="boolean" truevalue="-c" falsevalue="" label="Report contained genes?" help="Useful for CNVs
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46 but potentially long list of genes."/>
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47 </section>
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48 </xml>
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49 <xml name="s">
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50 <section name="s" title="SV annotation options" expanded="true">
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51 <param argument="--db" type="data" format="vcf,bcf" label="Select database file"/>
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52 <param argument="--bpoffset" type="integer" value="50" label="Set maximum breakpoint offset"/>
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53 <param argument="--ratio" type="float" min="0.0" max="1.0" value="0.8" label="Set minimum size ratio smaller SV to larger SV"/>
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54 <param argument="--strategy" type="select" label="Select matching strategy">
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55 <option value="best" selected="true">Best</option>
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56 <option value="all">All</option>
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57 </param>
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58 <param argument="--notype" type="boolean" truevalue="-n" falsevalue="" label="Require matching SV types?"/>
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59 <param argument="--nomatch" type="boolean" truevalue="-m" falsevalue="" label="Report SVs without match in database?"/>
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60 </section>
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61 </xml>
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62 </macros>