# HG changeset patch
# User iuc
# Date 1707651013 0
# Node ID 8dc7512c9dc97fde59ba606e97ecbca39681bbdc
# Parent  1dd7adc21b6d8e3e31d7b98070ea4f8eecfa501e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit 669dd4d406e86aee7d83e7420dced981c180d805

diff -r 1dd7adc21b6d -r 8dc7512c9dc9 gaeval.xml
--- a/gaeval.xml	Sun Jan 03 14:59:26 2021 +0000
+++ b/gaeval.xml	Sun Feb 11 11:30:13 2024 +0000
@@ -1,92 +1,92 @@
-<tool id="aegean_gaeval" name="AEGeAn GAEVAL" version="@TOOL_VERSION@" profile="20.01">
+<tool id="aegean_gaeval" name="AEGeAn GAEVAL" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <description> compute coverage and integrity scores for gene models using transcript alignments.</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>gaeval --version</version_command>
-    <command detect_errors='exit_code'>
+    <command detect_errors="exit_code">
         <![CDATA[
-            gaeval '$alignmentgff3' '$genesgff3' 
+            gaeval "$alignmentgff3" "$genesgff3" 
             -a $weights.alpha
             -b $weights.beta
             -g $weights.gamma
             -e $weights.epsilon
             -c $expected.expcds
             -5 $expected.exp5putr
-            -3 $expected.exp3putr > '$output'
+            -3 $expected.exp3putr > "$output"
             ]]>
     </command>
     <inputs>
-        <param name='alignmentgff3' type='data' format='gff3' label='Alignment GFF3 file' />
-        <param name='genesgff3' type='data' format='gff3' label='Genes GFF3 file'/>
+        <param name="alignmentgff3" type="data" format="gff3" label="Alignment GFF3 file" />
+        <param name="genesgff3" type="data" format="gff3" label="Genes GFF3 file"/>
         <!-- Weight options -->
-        <section name='weights'
-            title='Weights for calculating integrity score'
-            expanded='False'>
-            <param argument='--alpha' type='float'                
-                min='0' max='1' value='0.6' 
-                label='Introns confirmed, or % expected CDS lenght for single-exon genes'   
-                help='The percentage of introns confirmed by an alignment gap; for single-exon gene predictions lacking introns, it represents the ratio of the observed CDS length to the expected CDS length. '/>
-            <param argument='--beta' type='float'                
-                min='0' max='1' value='0.3' 
-                label='Exon coverage'   
-                help='Overall percentage of individual exons spanned by at least one sequencing read.'/>
-            <param argument='--gamma' type='float' 
-                min='0' max='1' value='0.05'
-                label='% expected 5’ UTR length'
-                help='The ratio of the observed 5’ UTR length to the expected 5’ UTR length.'/>
-            <param argument='--epsilon' type='float' 
-                min='0' max='1' value='0.05'
-                label='% expected 3’ UTR lenght'
-                help='The ratio of the observed 3’ UTR length to the expected 3’ UTR length.'/>
+        <section name="weights"
+            title="Weights for calculating integrity score"
+            expanded="False">
+            <param argument="--alpha" type="float"                
+                min="0" max="1" value="0.6" 
+                label="Introns confirmed, or % expected CDS lenght for single-exon genes"   
+                help="The percentage of introns confirmed by an alignment gap; for single-exon gene predictions lacking introns, it represents the ratio of the observed CDS length to the expected CDS length. "/>
+            <param argument="--beta" type="float"                
+                min="0" max="1" value="0.3" 
+                label="Exon coverage"   
+                help="Overall percentage of individual exons spanned by at least one sequencing read."/>
+            <param argument="--gamma" type="float" 
+                min="0" max="1" value="0.05"
+                label="% expected 5’ UTR length"
+                help="The ratio of the observed 5’ UTR length to the expected 5’ UTR length."/>
+            <param argument="--epsilon" type="float" 
+                min="0" max="1" value="0.05"
+                label="% expected 3’ UTR lenght"
+                help="The ratio of the observed 3’ UTR length to the expected 3’ UTR length."/>
         </section>
         <!-- Expected feature lenght options -->
-        <section name='expected'
-            title='Expected feature lenghts for calculating integrity score'
-            expanded='False'>
-            <param name='expcds' type='integer'
-                min='0' max='1000' value='400'
-                label='Expected CDs length (in bp) (-c)' />
-            <param name='exp5putr' type='integer' 
-                min='0' max='1000' value='200'
-                label='Expected 5’ UTR length (-5)' />
-            <param name='exp3putr' type='integer'
-                min='0' max='1000' value='100' 
-                label='Expected 3’ UTR length (-3)' />
+        <section name="expected"
+            title="Expected feature lenghts for calculating integrity score"
+            expanded="False">
+            <param name="expcds" type="integer"
+                min="0" max="1000" value="400"
+                label="Expected CDs length (in bp) (-c)" />
+            <param name="exp5putr" type="integer" 
+                min="0" max="1000" value="200"
+                label="Expected 5’ UTR length (-5)" />
+            <param name="exp3putr" type="integer"
+                min="0" max="1000" value="100" 
+                label="Expected 3’ UTR length (-3)" />
         </section>
     </inputs>
     <outputs>
-        <data name='output' format='tabular' />
+        <data name="output" format="tabular" />
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name='alignmentgff3' value='TAIR10_GFF3_alignment.gff'/>
-            <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/>
-            <output name='output' file='gaeval_output_test1.txt'/>
+            <param name="alignmentgff3" value="TAIR10_GFF3_alignment.gff" ftype="gff3"/>
+            <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
+            <output name="output" file="gaeval_output_test1.txt"/>
         </test>
         <test expect_num_outputs="1">
-            <param name='alignmentgff3' value='TAIR10_GFF3_alignment.gff'/>
-            <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/>
-            <section name='weights'>
-                <param name='alpha' value='0.5'/>
-                <param name='beta' value='0.4'/>
-                <param name='gamma' value='0.05'/>
-                <param name='epsion' value='0.05'/>
+            <param name="alignmentgff3" value="TAIR10_GFF3_alignment.gff" ftype="gff3"/>
+            <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
+            <section name="weights">
+                <param name="alpha" value="0.5"/>
+                <param name="beta" value="0.4"/>
+                <param name="gamma" value="0.05"/>
+                <param name="epsion" value="0.05"/>
             </section>
-            <output name='output' file='gaeval_output_test2.txt'/>
+            <output name="output" file="gaeval_output_test2.txt"/>
         </test>
         <test expect_num_outputs="1">
-            <param name='alignmentgff3' value='TAIR10_GFF3_alignment.gff'/>
-            <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/>
-            <section name='expected'>
-                <param name='expcds' value='20'/>
-                <param name='exp5putr' value='150'/>
-                <param name='exp3putr' value='120'/>
+            <param name="alignmentgff3" value="TAIR10_GFF3_alignment.gff" ftype="gff3"/>
+            <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
+            <section name="expected">
+                <param name="expcds" value="20"/>
+                <param name="exp5putr" value="150"/>
+                <param name="exp3putr" value="120"/>
             </section>
-            <output name='output' file='gaeval_output_test3.txt' lines_diff='2'/>
+            <output name="output" file="gaeval_output_test3.txt" lines_diff="2"/>
         </test>
 
     </tests>
@@ -126,5 +126,5 @@
             
 ]]>
     </help>
-    <expand macro='citations'/>
+    <expand macro="citations"/>
 </tool>
diff -r 1dd7adc21b6d -r 8dc7512c9dc9 macros.xml
--- a/macros.xml	Sun Jan 03 14:59:26 2021 +0000
+++ b/macros.xml	Sun Feb 11 11:30:13 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>