changeset 1:c45c9dd066e2 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit 669dd4d406e86aee7d83e7420dced981c180d805

--- a/canongff3.xml	Sun Jan 03 14:58:31 2021 +0000
+++ b/canongff3.xml	Sun Feb 11 11:29:29 2024 +0000
@@ -1,53 +1,53 @@
-<tool id='aegean_canongff3' name=' AEGeAn CanonGFF3' version='@TOOL_VERSION@' profile='20.01'>
+<tool id="aegean_canongff3" name="AEGeAn CanonGFF3" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <description> pre-process GFF3 files, removing all features not directly related to protein-coding genes</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>canon-gff3 --version</version_command>
-    <command detect_errors='exit_code'>
+    <command detect_errors="exit_code">
         <![CDATA[
-            canon-gff3 '$gff3file'
+            canon-gff3 "$gff3file"
             $infer
             #if $source
-                -s '$source'
+                -s "$source"
             #end if
-            -o '$output'
+            -o "$output"
             ]]>
     </command>
     <inputs>
-        <param name='gff3file' type='data' format='gff3' label='GFF3 File'
-            help="GFF3 annotation file" multiple='true' />
-        <param argument='--infer' type='boolean'
-            truevalue='--infer' falsevalue=''
-            label='Infer gene feature for transcripts lacking it'            
-            help='For transcript features lacking an explicitly declared gene feature as a parent, create this feature on-they-fly'/>
-        <param argument='--source' type='text'
-            value='' optional='true' 
-            label='Reset the source of each feature'
-            help='Reset the source of each feature to the given value. Source keywords can be a program (e.g. RepeatMasker) or an organization (like TAIR)'>
+        <param name="gff3file" type="data" format="gff3" label="GFF3 File"
+            help="GFF3 annotation file" multiple="true" />
+        <param argument="--infer" type="boolean"
+            truevalue="--infer" falsevalue=""
+            label="Infer gene feature for transcripts lacking it"            
+            help="For transcript features lacking an explicitly declared gene feature as a parent, create this feature on-they-fly"/>
+        <param argument="--source" type="text"
+            value="" optional="true" 
+            label="Reset the source of each feature"
+            help="Reset the source of each feature to the given value. Source keywords can be a program (e.g. RepeatMasker) or an organization (like TAIR)">
           <validator type="regex" message="Please only use letters, numbers or underscores in sample label">^[\w]+$</validator>
         </param>
     </inputs>
     <outputs>
-        <data name='output' format='gff3' />
+        <data name="output" format="gff3" />
     </outputs>
     <tests>
         <test>
-            <param name='gff3file' value='TAIR10_GFF3_genes.gff'/>
-            <output name='output' file='canon-output_test1.gff3'/>
+            <param name="gff3file" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
+            <output name="output" file="canon-output_test1.gff3"/>
         </test>
         <test>
-            <param name='gff3file' value='TAIR10_GFF3_genes.gff'/>
-            <param name='source' value='test_source'/>
-            <output name='output' file='canon-output_test2.gff3'/>
+            <param name="gff3file" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
+            <param name="source" value="test_source"/>
+            <output name="output" file="canon-output_test2.gff3"/>
         </test>
         <test>
-            <param name='gff3file' value='TAIR10_GFF3_genes.gff'/>
-            <param name='infer' value='true'/>
-            <output name='output' file='canon-output_test3.gff3'/>
+            <param name="gff3file" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
+            <param name="infer" value="true"/>
+            <output name="output" file="canon-output_test3.gff3"/>
         </test>
     </tests>
     <help>
@@ -78,5 +78,5 @@
             
 ]]>
     </help>
-    <expand macro='citations'/>
+    <expand macro="citations"/>
 </tool>

--- a/macros.xml	Sun Jan 03 14:58:31 2021 +0000
+++ b/macros.xml	Sun Feb 11 11:29:29 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>