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annotate macros.xml @ 0:f7c0a0030254 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
author bgruening
date Tue, 23 May 2023 13:43:07 +0000
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children 6d8444408ff1
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f7c0a0030254 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
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1 <macros>
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2 <token name="@TOOL_VERSION@">1.1.0</token>
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3 <token name="@VERSION_SUFFIX@">0</token>
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="@TOOL_VERSION@">agat</requirement>
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7 <requirement type="package" version="0.34">perl-statistics-r</requirement>
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8 </requirements>
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9 </xml>
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10 <xml name="biotools">
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11 <xrefs>
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12 <xref type="bio.tools">agat</xref>
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13 </xrefs>
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14 </xml>
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15 <xml name="citations">
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16 <citations>
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17 <citation type="doi">10.5281/zenodo.3552717</citation>
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18 </citations>
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19 </xml>
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20 <xml name="ANNOTATION_INPUT" token_format="gff,gtf,gff3,gff3.gz">
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21 <param argument="--gff" type="data" format="@FORMAT@" label="Annotation file" help="Input GTF/GFF file" />
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22 </xml>
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23
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24 <xml name="REFERENCE_FASTA">
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25 <conditional name="reference_genome">
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26 <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options.">
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27 <option value="indexed" selected="true">Use a built-in genome</option>
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28 <option value="history" selected="true">Use a genome from history</option>
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29 </param>
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30 <when value="indexed">
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31 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team.">
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32 <options from_data_table="fasta_indexes">
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33 <filter type="sort_by" column="2" />
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34 <validator type="no_options" message="No genomes are available for the selected input dataset" />
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35 </options>
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36 </param>
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37 </when>
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38 <when value="history">
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39 <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format" />
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40 </when>
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41 </conditional>
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42 </xml>
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43 <token name="@input_annotation_single@"><![CDATA[
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44 #set $input_annotation = 'annotation.' + str($tool.gff.ext)
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45 ln -s '${tool.gff}' $input_annotation &&
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46 ]]></token>
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47 <token name="@input_reference@"><![CDATA[
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48 #if $tool.reference_genome.source == 'history':
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49 #set $ref_genome = 'reference.fasta'
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50 ln -s -f '${tool.reference_genome.history_item}' $ref_genome &&
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51 #else:
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52 #set $ref_genome = $tool.reference_genome.index.fields.path
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53 #end if
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54 ]]></token>
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55 <token name="@input_annotation_double@"><![CDATA[
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56 #set $input1 = 'annotation1.' + str($tool.input_annotation1.ext)
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57 #set $input2 = 'annotation2.' + str($tool.input_annotation2.ext)
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58 ln -s '${tool.input_annotation1}' $input1 &&
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59 ln -s '${tool.input_annotation2}' $input2 &&
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60 ]]></token>
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61
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62
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63 </macros>