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changeset 1:1fdc517743e6 draft default tip

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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(-) [+]
line wrap: on
line diff
--- 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 &quot;locus%lu&quot; (locus1, locus2, etc) for loci and &quot;iLocus%lu&quot; (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>