Mercurial > repos > bgruening > agat
diff macros.xml @ 0:f7c0a0030254 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
author | bgruening |
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date | Tue, 23 May 2023 13:43:07 +0000 |
parents | |
children | 6d8444408ff1 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue May 23 13:43:07 2023 +0000 @@ -0,0 +1,63 @@ +<macros> + <token name="@TOOL_VERSION@">1.1.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">agat</requirement> + <requirement type="package" version="0.34">perl-statistics-r</requirement> + </requirements> + </xml> + <xml name="biotools"> + <xrefs> + <xref type="bio.tools">agat</xref> + </xrefs> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.5281/zenodo.3552717</citation> + </citations> + </xml> + <xml name="ANNOTATION_INPUT" token_format="gff,gtf,gff3,gff3.gz"> + <param argument="--gff" type="data" format="@FORMAT@" label="Annotation file" help="Input GTF/GFF file" /> + </xml> + + <xml name="REFERENCE_FASTA"> + <conditional name="reference_genome"> + <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options."> + <option value="indexed" selected="true">Use a built-in genome</option> + <option value="history" selected="true">Use a genome from history</option> + </param> + <when value="indexed"> + <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team."> + <options from_data_table="fasta_indexes"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No genomes are available for the selected input dataset" /> + </options> + </param> + </when> + <when value="history"> + <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format" /> + </when> + </conditional> + </xml> + <token name="@input_annotation_single@"><![CDATA[ + #set $input_annotation = 'annotation.' + str($tool.gff.ext) + ln -s '${tool.gff}' $input_annotation && + ]]></token> + <token name="@input_reference@"><![CDATA[ + #if $tool.reference_genome.source == 'history': + #set $ref_genome = 'reference.fasta' + ln -s -f '${tool.reference_genome.history_item}' $ref_genome && + #else: + #set $ref_genome = $tool.reference_genome.index.fields.path + #end if + ]]></token> + <token name="@input_annotation_double@"><![CDATA[ + #set $input1 = 'annotation1.' + str($tool.input_annotation1.ext) + #set $input2 = 'annotation2.' + str($tool.input_annotation2.ext) + ln -s '${tool.input_annotation1}' $input1 && + ln -s '${tool.input_annotation2}' $input2 && + ]]></token> + + +</macros>