Mercurial > repos > iuc > aegean_locuspocus
changeset 1:1fdc517743e6 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit 669dd4d406e86aee7d83e7420dced981c180d805
| author | iuc |
|---|---|
| date | Sun, 11 Feb 2024 11:29:44 +0000 |
| parents | c4ac24510b55 |
| children | |
| files | locuspocus.xml macros.xml |
| diffstat | 2 files changed, 128 insertions(+), 128 deletions(-) [+] |
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--- a/locuspocus.xml Sun Jan 03 14:58:58 2021 +0000 +++ b/locuspocus.xml Sun Feb 11 11:29:44 2024 +0000 @@ -1,15 +1,15 @@ -<tool id='aegean_locuspocus' name='AEGeAn LocusPocus' version='@TOOL_VERSION@' profile='20.01'> +<tool id="aegean_locuspocus" name="AEGeAn LocusPocus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> <description> calculate locus coordinates for the given gene annotation</description> <macros> <import>macros.xml</import> </macros> - <expand macro='xrefs'/> - <expand macro='edam_ontology'/> - <expand macro='requirements'/> + <expand macro="edam_ontology"/> + <expand macro="xrefs"/> + <expand macro="requirements"/> <version_command>locuspocus --version</version_command> - <command detect_errors='exit_code'> + <command detect_errors="exit_code"> <![CDATA[ - locuspocus '$genesgff3' + locuspocus "$genesgff3" -l $ilocus_parsing.delta $ilocus_parsing.mode $ilocus_parsing.skipiloci @@ -17,88 +17,88 @@ $refine_options.refine_parameters.cds #end if -m $refine_options.minoverlap - -f '$input_options.filter' + -f "$input_options.filter" #if $input_options.parent - -p '$input_options.parent' + -p "$input_options.parent" #end if $input_options.pseudo #if $output_options.outputfiles #if "ilens" in $output_options.outputfiles - --ilens '$output_ilens' + --ilens "$output_ilens" #end if #if "genemap" in $output_options.outputfiles - --genemap '$output_genemap' + --genemap "$output_genemap" #end if #if "transmap" in $output_options.outputfiles - --transmap '$output_transmap' + --transmap "$output_transmap" #end if #end if #if $output_options.namefmt - -n '$output_options.namefmt' + -n "$output_options.namefmt" #end if $output_options.retainids - -o '$output' + -o "$output" ]]> </command> <inputs> - <param name='genesgff3' type='data' format='gff3' label="GFF3 File" /> - <section name='ilocus_parsing' title='iLocus parsing options' expanded='True'> - <param argument='--delta' type='integer' - min='0' max='1000' value='500' - label='Gene loci extension' - help='When parsing interval loci, use the following delta to extend gene loci and include potential regulatory regions' /> - <param name='mode' type='select' label='Annotation mode'> - <option value='' selected='true'>Default mode</option> - <option value='--skipends'> Exclude unannotated iLoci at either end of the sequence</option> - <option value='--endsonly'> Report only incomplete iLocus fragments at the unannotated ends of sequences</option> + <param name="genesgff3" type="data" format="gff3" label="GFF3 File" /> + <section name="ilocus_parsing" title="iLocus parsing options" expanded="True"> + <param argument="--delta" type="integer" + min="0" max="1000" value="500" + label="Gene loci extension" + help="When parsing interval loci, use the following delta to extend gene loci and include potential regulatory regions" /> + <param name="mode" type="select" label="Annotation mode"> + <option value="" selected="true">Default mode</option> + <option value="--skipends"> Exclude unannotated iLoci at either end of the sequence</option> + <option value="--endsonly"> Report only incomplete iLocus fragments at the unannotated ends of sequences</option> </param> - <param argument="--skipiloci" type='boolean' - truevalue='--skipiiloci' falsevalue='' - label='Do not report intergenic iLoci' /> + <param argument="--skipiloci" type="boolean" + truevalue="--skipiiloci" falsevalue="" + label="Do not report intergenic iLoci" /> </section> - <section name='refine_options' title='Refine options' expanded='false'> - <conditional name='refine_parameters'> - <param name='refine' type='select' - label='Mode for handling of overlpping genes' - help='Refine mode allows for a more nuanced handling of overlapping genes.'> - <option value=''>Default</option> - <option value='--refine'>Refine mode</option> + <section name="refine_options" title="Refine options" expanded="false"> + <conditional name="refine_parameters"> + <param name="refine" type="select" + label="Mode for handling of overlpping genes" + help="Refine mode allows for a more nuanced handling of overlapping genes."> + <option value="">Default</option> + <option value="--refine">Refine mode</option> </param> - <when value=''/> - <when value='--refine'> - <param argument='--cds' type='boolean' - truevalue='--cds' falsevalue='' - label='Use CDS rather than UTRs' - help='(-c)' /> + <when value=""/> + <when value="--refine"> + <param argument="--cds" type="boolean" + truevalue="--cds" falsevalue="" + label="Use CDS rather than UTRs" + help="(-c)" /> </when> </conditional> - <param argument='--minoverlap' type='integer' - max='20' min='1' value='1' - label='Minimum number of overlapping nucleotides' - help='The minimum number of nucleotides two genes must overlap to be grouped in the same iLocus' /> + <param argument="--minoverlap" type="integer" + max="20" min="1" value="1" + label="Minimum number of overlapping nucleotides" + help="The minimum number of nucleotides two genes must overlap to be grouped in the same iLocus" /> </section> - <section name='input_options' title='Input options' expanded='false'> - <param argument='--filter' type='text' - value='gene' - label='Comma-separated list of feature types to use' + <section name="input_options" title="Input options" expanded="false"> + <param argument="--filter" type="text" + value="gene" + label="Comma-separated list of feature types to use" help="Select the featured used to annotate intervals on a genome (e.g. gene, intron, exon)." /> - <param argument='--parent' type='text' - value='' optional='true' - label='Create a parent for features that lack a parent feature' - help='If a feature of type $CT exists without a parent, create a parent for this feature with type $PT; for example, mRNA:gene will create a gene feature as a parent for any top-level mRNA feature.'/> - <param argument='--pseudo' type='boolean' - truevalue='--pseudo' falsevalue='' - label='Correct erroneously labeled pseudogenes'/> + <param argument="--parent" type="text" + value="" optional="true" + label="Create a parent for features that lack a parent feature" + help="If a feature of type $CT exists without a parent, create a parent for this feature with type $PT; for example, mRNA:gene will create a gene feature as a parent for any top-level mRNA feature."/> + <param argument="--pseudo" type="boolean" + truevalue="--pseudo" falsevalue="" + label="Correct erroneously labeled pseudogenes"/> </section> - <section name='output_options' title='Output options' expanded='false'> - <param argument='--retainids' type='boolean' - truevalue='--retainids' falsevalue='' - label='Retain original feature IDs' - help='Retain original feature IDs from input files; conflicts will arise if input contains duplicated ID values'/> - <param argument='--namefmt' type='text' - value='' optional='true' - label='ID format for newly created locy' - help='Provide a format string to override the default ID format for newly created loci; default is "locus%lu" (locus1, locus2, etc) for loci and "iLocus%lu" (iLocus1, iLocus2, etc) for interval loci; note the format string should include a single %lu specifier to be filled in with a long unsigned integer value.'/> + <section name="output_options" title="Output options" expanded="false"> + <param argument="--retainids" type="boolean" + truevalue="--retainids" falsevalue="" + label="Retain original feature IDs" + help="Retain original feature IDs from input files; conflicts will arise if input contains duplicated ID values"/> + <param argument="--namefmt" type="text" + value="" optional="true" + label="ID format for newly created locy" + help="Provide a format string to override the default ID format for newly created loci; default is "locus%lu" (locus1, locus2, etc) for loci and "iLocus%lu" (iLocus1, iLocus2, etc) for interval loci; note the format string should include a single %lu specifier to be filled in with a long unsigned integer value."/> <param name="outputfiles" type="select" display="checkboxes" label="Output files" multiple="true" optional="true" > <option value="ilens">Create file with the lenghts of each intergenic iLocus</option> @@ -109,97 +109,97 @@ </inputs> <outputs> - <data name='output' format='tabular' /> - <data name='output_ilens' format='tabular'> - <filter>output_options['outputfiles'] and "ilens" in output_options['outputfiles']</filter> + <data name="output" format="tabular" /> + <data name="output_ilens" format="tabular" label="${tool.name} on ${on_string}: Intergenic regions lengths"> + <filter>output_options["outputfiles"] and "ilens" in output_options["outputfiles"]</filter> </data> - <data name='output_genemap' format='tabular'> - <filter>output_options['outputfiles'] and "genemap" in output_options['outputfiles']</filter> + <data name="output_genemap" format="tabular" label="${tool.name} on ${on_string}: Annotation locus mapping"> + <filter>output_options["outputfiles"] and "genemap" in output_options["outputfiles"]</filter> </data> - <data name='output_transmap' format='tabular'> - <filter>output_options['outputfiles'] and "transmap" in output_options['outputfiles']</filter> + <data name="output_transmap" format="tabular" label="${tool.name} on ${on_string}: Transcript locus mapping"> + <filter>output_options["outputfiles"] and "transmap" in output_options["outputfiles"]</filter> </data> </outputs> <tests> <test expect_num_outputs="1"> - <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/> - <output name='output' file='locuspocus_output_test1.txt'/> + <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/> + <output name="output" file="locuspocus_output_test1.txt"/> </test> <test expect_num_outputs="1"> - <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/> - <section name='ilocus_parsing'> - <param name='delta' value='400'/> - <param name='mode' value='--skipends'/> + <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/> + <section name="ilocus_parsing"> + <param name="delta" value="400"/> + <param name="mode" value="--skipends"/> </section> - <output name='output' file='locuspocus_output_test2.txt'/> + <output name="output" file="locuspocus_output_test2.txt"/> </test> <test expect_num_outputs="1"> - <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/> - <section name='ilocus_parsing'> - <param name='skipiloci' value='true'/> - <param name='mode' value='--endsonly'/> + <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/> + <section name="ilocus_parsing"> + <param name="skipiloci" value="true"/> + <param name="mode" value="--endsonly"/> </section> - <output name='output' file='locuspocus_output_test3.txt'/> + <output name="output" file="locuspocus_output_test3.txt"/> </test> <test expect_num_outputs="1"> - <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/> - <section name='refine_options'> - <param name='refine_parameters|refine' value='--refine'/> - <param name='minoverlap' value='5'/> + <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/> + <section name="refine_options"> + <param name="refine_parameters|refine" value="--refine"/> + <param name="minoverlap" value="5"/> </section> - <output name='output' file='locuspocus_output_test4.txt'/> + <output name="output" file="locuspocus_output_test4.txt"/> </test> <test expect_num_outputs="1"> - <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/> - <section name='input_options'> - <param name='filter' value='gene,intron'/> - <param name='parent' value='mRNA:gene'/> + <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/> + <section name="input_options"> + <param name="filter" value="gene,intron"/> + <param name="parent" value="mRNA:gene"/> </section> - <output name='output' file='locuspocus_output_test5.txt'/> + <output name="output" file="locuspocus_output_test5.txt"/> </test> <test expect_num_outputs="1"> - <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/> - <section name='input_options'> - <param name='filter' value='gene,intron'/> - <param name='parent' value='mRNA:gene'/> - <param name='pseudo' value='true'/> + <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/> + <section name="input_options"> + <param name="filter" value="gene,intron"/> + <param name="parent" value="mRNA:gene"/> + <param name="pseudo" value="true"/> </section> - <output name='output' file='locuspocus_output_test6.txt'/> + <output name="output" file="locuspocus_output_test6.txt"/> </test> <test expect_num_outputs="4"> - <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/> - <section name='output_options'> - <param name='retainids' value='true'/> - <param name='namefmt' value='test%lu'/> - <param name='outputfiles' value='ilens,genemap,transmap'/> + <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/> + <section name="output_options"> + <param name="retainids" value="true"/> + <param name="namefmt" value="test%lu"/> + <param name="outputfiles" value="ilens,genemap,transmap"/> </section> - <output name='output' file='locuspocus_output_test7.txt'/> - <output name='output_ilens' file='locuspocus_lenght_test7.txt'/> - <output name='output_genemap' file='locuspocus_genemap_test7.txt'/> - <output name='output_transmap' file='locuspocus_transmap_test7.txt'/> + <output name="output" file="locuspocus_output_test7.txt"/> + <output name="output_ilens" file="locuspocus_lenght_test7.txt"/> + <output name="output_genemap" file="locuspocus_genemap_test7.txt"/> + <output name="output_transmap" file="locuspocus_transmap_test7.txt"/> </test> <test expect_num_outputs="4"> - <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/> - <section name='refine_options'> - <param name='refine_parameters|refine' value='--refine'/> - <param name='refine_options|minoverlap' value='5'/> + <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/> + <section name="refine_options"> + <param name="refine_parameters|refine" value="--refine"/> + <param name="refine_options|minoverlap" value="5"/> </section> - <section name='ilocus_parsing'> - <param name='delta' value='400'/> - <param name='mode' value='--skipends'/> + <section name="ilocus_parsing"> + <param name="delta" value="400"/> + <param name="mode" value="--skipends"/> </section> - <section name='input_options'> - <param name='filter' value='gene,intron'/> - <param name='parent' value='mRNA:gene'/> + <section name="input_options"> + <param name="filter" value="gene,intron"/> + <param name="parent" value="mRNA:gene"/> </section> - <section name='output_options'> - <param name='retainids' value='true'/> - <param name='outputfiles' value='ilens,genemap,transmap'/> + <section name="output_options"> + <param name="retainids" value="true"/> + <param name="outputfiles" value="ilens,genemap,transmap"/> </section> - <output name='output' file='locuspocus_output_test8.txt'/> - <output name='output_ilens' file='locuspocus_lenght_test8.txt'/> - <output name='output_genemap' file='locuspocus_genemap_test8.txt'/> - <output name='output_transmap' file='locuspocus_transmap_test8.txt'/> + <output name="output" file="locuspocus_output_test8.txt"/> + <output name="output_ilens" file="locuspocus_lenght_test8.txt"/> + <output name="output_genemap" file="locuspocus_genemap_test8.txt"/> + <output name="output_transmap" file="locuspocus_transmap_test8.txt"/> </test> </tests> <help> @@ -232,5 +232,5 @@ ]]> </help> - <expand macro='citations'/> + <expand macro="citations"/> </tool>
--- a/macros.xml Sun Jan 03 14:58:58 2021 +0000 +++ b/macros.xml Sun Feb 11 11:29:44 2024 +0000 @@ -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>