| Previous changeset 0:c4ac24510b55 (2021-01-03) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit 669dd4d406e86aee7d83e7420dced981c180d805 |
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modified:
locuspocus.xml macros.xml |
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| diff -r c4ac24510b55 -r 1fdc517743e6 locuspocus.xml --- a/locuspocus.xml Sun Jan 03 14:58:58 2021 +0000 +++ b/locuspocus.xml Sun Feb 11 11:29:44 2024 +0000 |
| [ |
| b'@@ -1,15 +1,15 @@\n-<tool id=\'aegean_locuspocus\' name=\'AEGeAn LocusPocus\' version=\'@TOOL_VERSION@\' profile=\'20.01\'>\n+<tool id="aegean_locuspocus" name="AEGeAn LocusPocus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">\n <description> calculate locus coordinates for the given gene annotation</description>\n <macros> \n <import>macros.xml</import>\n </macros> \n- <expand macro=\'xrefs\'/>\n- <expand macro=\'edam_ontology\'/>\n- <expand macro=\'requirements\'/>\n+ <expand macro="edam_ontology"/>\n+ <expand macro="xrefs"/>\n+ <expand macro="requirements"/>\n <version_command>locuspocus --version</version_command>\n- <command detect_errors=\'exit_code\'>\n+ <command detect_errors="exit_code">\n <![CDATA[\n- locuspocus \'$genesgff3\'\n+ locuspocus "$genesgff3"\n -l $ilocus_parsing.delta\n $ilocus_parsing.mode\n $ilocus_parsing.skipiloci\n@@ -17,88 +17,88 @@\n $refine_options.refine_parameters.cds\n #end if \n -m $refine_options.minoverlap\n- -f \'$input_options.filter\'\n+ -f "$input_options.filter"\n #if $input_options.parent\n- -p \'$input_options.parent\'\n+ -p "$input_options.parent"\n #end if\n $input_options.pseudo\n #if $output_options.outputfiles\n \t #if "ilens" in $output_options.outputfiles\n- --ilens \'$output_ilens\'\n+ --ilens "$output_ilens"\n #end if\n #if "genemap" in $output_options.outputfiles\n- --genemap \'$output_genemap\'\n+ --genemap "$output_genemap"\n #end if\n #if "transmap" in $output_options.outputfiles\n- --transmap \'$output_transmap\'\n+ --transmap "$output_transmap"\n #end if\n #end if\n #if $output_options.namefmt\n- -n \'$output_options.namefmt\'\n+ -n "$output_options.namefmt"\n #end if\n $output_options.retainids\n- -o \'$output\'\n+ -o "$output"\n ]]>\n </command>\n <inputs>\n- <param name=\'genesgff3\' type=\'data\' format=\'gff3\' label="GFF3 File" />\n- <section name=\'ilocus_parsing\' title=\'iLocus parsing options\' expanded=\'True\'>\n- <param argument=\'--delta\' type=\'integer\' \n- min=\'0\' max=\'1000\' value=\'500\'\n- label=\'Gene loci extension\'\n- help=\'When parsing interval loci, use the following delta to extend gene loci and include potential regulatory regions\' />\n- <param name=\'mode\' type=\'select\' label=\'Annotation mode\'>\n- <option value=\'\' selected=\'true\'>Default mode</option>\n- <option value=\'--skipends\'> Exclude unannotated iLoci at either end of the sequence</option>\n- <option value=\'--endsonly\'> Report only incomplete iLocus fragments at the unannotated ends of sequences</option>\n+ <param name="genesgff3" type="data" format="gff3" label="GFF3 File" />\n+ <section name="ilocus_parsing" title="iLocus parsing options" expanded="True">\n+ <param argument="--delta" type="integer" \n+ min="0" max="1000" value="500"\n+ label="Gene loci extension"\n+ help="When parsing interval loci, use the following delta to extend gene loci and include potential regulatory regions" />\n+ <param name="mode" type="select" label="Annotation mode">\n+ <option value="" selected="true">Default mode</option>\n+ <option value="--skipends"> Exclude unannotated iLoci at either end of the sequence</option>\n+ <'..b' <param name="pseudo" value="true"/>\n </section>\t \n- <output name=\'output\' file=\'locuspocus_output_test6.txt\'/>\n+ <output name="output" file="locuspocus_output_test6.txt"/>\n </test>\n <test expect_num_outputs="4">\n- <param name=\'genesgff3\' value=\'TAIR10_GFF3_genes.gff\'/>\n- <section name=\'output_options\'>\n- <param name=\'retainids\' value=\'true\'/>\n- <param name=\'namefmt\' value=\'test%lu\'/>\n- <param name=\'outputfiles\' value=\'ilens,genemap,transmap\'/>\n+ <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>\n+ <section name="output_options">\n+ <param name="retainids" value="true"/>\n+ <param name="namefmt" value="test%lu"/>\n+ <param name="outputfiles" value="ilens,genemap,transmap"/>\n </section>\n- <output name=\'output\' file=\'locuspocus_output_test7.txt\'/>\n- <output name=\'output_ilens\' file=\'locuspocus_lenght_test7.txt\'/>\n- <output name=\'output_genemap\' file=\'locuspocus_genemap_test7.txt\'/>\n- <output name=\'output_transmap\' file=\'locuspocus_transmap_test7.txt\'/>\n+ <output name="output" file="locuspocus_output_test7.txt"/>\n+ <output name="output_ilens" file="locuspocus_lenght_test7.txt"/>\n+ <output name="output_genemap" file="locuspocus_genemap_test7.txt"/>\n+ <output name="output_transmap" file="locuspocus_transmap_test7.txt"/>\n </test>\n <test expect_num_outputs="4">\n- <param name=\'genesgff3\' value=\'TAIR10_GFF3_genes.gff\'/>\n-\t <section name=\'refine_options\'>\n- <param name=\'refine_parameters|refine\' value=\'--refine\'/>\n- <param name=\'refine_options|minoverlap\' value=\'5\'/>\n+ <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>\n+\t <section name="refine_options">\n+ <param name="refine_parameters|refine" value="--refine"/>\n+ <param name="refine_options|minoverlap" value="5"/>\n \t </section>\n- <section name=\'ilocus_parsing\'>\n- <param name=\'delta\' value=\'400\'/>\n- <param name=\'mode\' value=\'--skipends\'/>\n+ <section name="ilocus_parsing">\n+ <param name="delta" value="400"/>\n+ <param name="mode" value="--skipends"/>\n </section>\n- <section name=\'input_options\'>\n- <param name=\'filter\' value=\'gene,intron\'/>\n- <param name=\'parent\' value=\'mRNA:gene\'/>\n+ <section name="input_options">\n+ <param name="filter" value="gene,intron"/>\n+ <param name="parent" value="mRNA:gene"/>\n </section>\t \n- <section name=\'output_options\'>\n- <param name=\'retainids\' value=\'true\'/>\n- <param name=\'outputfiles\' value=\'ilens,genemap,transmap\'/>\n+ <section name="output_options">\n+ <param name="retainids" value="true"/>\n+ <param name="outputfiles" value="ilens,genemap,transmap"/>\n </section>\n- <output name=\'output\' file=\'locuspocus_output_test8.txt\'/>\n- <output name=\'output_ilens\' file=\'locuspocus_lenght_test8.txt\'/>\n- <output name=\'output_genemap\' file=\'locuspocus_genemap_test8.txt\'/>\n- <output name=\'output_transmap\' file=\'locuspocus_transmap_test8.txt\'/>\n+ <output name="output" file="locuspocus_output_test8.txt"/>\n+ <output name="output_ilens" file="locuspocus_lenght_test8.txt"/>\n+ <output name="output_genemap" file="locuspocus_genemap_test8.txt"/>\n+ <output name="output_transmap" file="locuspocus_transmap_test8.txt"/>\n </test>\n </tests>\n <help>\n@@ -232,5 +232,5 @@\n \n ]]>\n </help>\n- <expand macro=\'citations\'/>\n+ <expand macro="citations"/>\n </tool>\n' |
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| diff -r c4ac24510b55 -r 1fdc517743e6 macros.xml --- a/macros.xml Sun Jan 03 14:58:58 2021 +0000 +++ b/macros.xml Sun Feb 11 11:29:44 2024 +0000 |
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| @@ -9,12 +9,12 @@ </xml> <xml name="xrefs"> <xrefs> - <xref type='bio.tools'>gaeval</xref> + <xref type="bio.tools">gaeval</xref> </xrefs> </xml> <xml name="requirements"> <requirements> - <requirement type="package" version="0.16.0">aegean</requirement> + <requirement type="package" version="@TOOL_VERSION@">aegean</requirement> </requirements> </xml> <xml name="citations"> @@ -32,5 +32,5 @@ </citations> </xml> <token name="@TOOL_VERSION@">0.16.0</token> - + <token name="@VERSION_SUFFIX@">1</token> </macros> |