diff parseval.xml @ 1:d6c074a93c51 draft default tip

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

--- a/parseval.xml	Sun Jan 03 14:58:02 2021 +0000
+++ b/parseval.xml	Sun Feb 11 11:29:58 2024 +0000
@@ -1,110 +1,110 @@
-<tool id='aegean_parseval' name='AEGeAn ParsEval' version='@TOOL_VERSION@' profile='20.01'>
+<tool id="aegean_parseval" name="AEGeAn ParsEval" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <description> compare two sets of gene annotations for the same sequence.</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>parseval --version</version_command>
-    <command detect_errors='exit_code'>
+    <command detect_errors="exit_code">
         <![CDATA[
-            #if $output_type == 'html'
-                mkdir -p '${output_html.extra_files_path}' &&
+            #if $output_type == "html"
+                mkdir -p "${output_html.extra_files_path}" &&
             #end if
-            parseval '$referencegff3' '$predictiongff3' 
+            parseval "$referencegff3" "$predictiongff3" 
             --delta $delta
             --maxtrans $maxtrans
             -w
             #if $refrlabel
-                --refrlabel '$refrlabel'
+                --refrlabel "$refrlabel"
             #end if
             #if $predlabel
-                --predlabel '$predlabel'
+                --predlabel "$predlabel"
             #end if
-            #if $output_type =='text'
-                -f 'text'
-                -o '$output_txt'
-            #else if $output_type == 'html'
-                -f 'html' 
-                -o '${output_html.files_path}'  &&
-                echo "</div> </body> </html>" >> '${output_html.files_path}'/index.html &&
-                cp '${output_html.files_path}'/index.html '$output_html'
+            #if $output_type =="text"
+                -f "text"
+                -o "$output_txt"
+            #else if $output_type == "html"
+                -f "html" 
+                -o "${output_html.files_path}"  &&
+                echo "</div> </body> </html>" >> "${output_html.files_path}"/index.html &&
+                cp "${output_html.files_path}"/index.html "$output_html"
             #end if
             ]]>
     </command>
     <inputs>
-        <param name='referencegff3' type='data'  format='gff3' label="Reference GFF3 file"/>
-        <param name='predictiongff3' type='data'  format='gff3' label="Prediction GFF3 file"/>
-        <param argument='--delta' type='integer'
-            min='0' max='20' value='0' 
-            label='Number of nucleotides to extend gene loci'/>
-        <param argument='--maxtrans' type='integer' 
-            min='1' max='50' value='32'
-            label='Maximum transcript allowed per locus' />
-        <param name='output_type' type='select'
-            label='Select the output type'>
-            <option value='text'>Text</option>
-            <option value='html'>HTML</option>
+        <param name="referencegff3" type="data"  format="gff3" label="Reference GFF3 file"/>
+        <param name="predictiongff3" type="data"  format="gff3" label="Prediction GFF3 file"/>
+        <param argument="--delta" type="integer"
+            min="0" max="20" value="0" 
+            label="Number of nucleotides to extend gene loci"/>
+        <param argument="--maxtrans" type="integer" 
+            min="1" max="50" value="32"
+            label="Maximum transcript allowed per locus" />
+        <param name="output_type" type="select"
+            label="Select the output type">
+            <option value="text">Text</option>
+            <option value="html">HTML</option>
         </param>
-        <param argument='--refrlabel' type='text'
-            value='' optional='true'
-            label='Reference annotations'
-            help='Optional label for reference annotations'/>
-        <param argument='--predlabel' type='text'
-            value='' optional='true'
-            label='Prediction annotations'
-            help='Optional label for prediction annotations'/>
+        <param argument="--refrlabel" type="text"
+            value="" optional="true"
+            label="Reference annotations"
+            help="Optional label for reference annotations"/>
+        <param argument="--predlabel" type="text"
+            value="" optional="true"
+            label="Prediction annotations"
+            help="Optional label for prediction annotations"/>
     </inputs>
     <outputs>
-        <data name='output_txt' format='txt'>
-            <filter>output_type == 'text'</filter>
+        <data name="output_txt" format="txt" label="${tool.name} on ${on_string}: text">
+            <filter>output_type == "text"</filter>
         </data>
-        <data name='output_html' format='html' from_work_dir="output.html">
-            <filter>output_type == 'html'</filter>
+        <data name="output_html" format="html" from_work_dir="output.html" label="${tool.name} on ${on_string}: HTML">
+            <filter>output_type == "html"</filter>
         </data>
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/>
-            <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/>
-            <param name='delta' value='5'/>
-            <param name='maxtrans' value='20'/>
-            <output name='output_txt' file='parseval_output_test1.txt' lines_diff='8'/>
+            <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
+            <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
+            <param name="delta" value="5"/>
+            <param name="maxtrans" value="20"/>
+            <output name="output_txt" file="parseval_output_test1.txt" lines_diff="8"/>
         </test>
         <test expect_num_outputs="1">
-            <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/>
-            <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/>
-            <output name='output_txt' file='parseval_output_test2.txt' lines_diff='8'/>
+            <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
+            <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
+            <output name="output_txt" file="parseval_output_test2.txt" lines_diff="8"/>
         </test>
         <test expect_num_outputs="1">
-            <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/>
-            <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/>
-            <param name='delta' value='10'/>
-            <param name='maxtrans' value='10'/>
-            <output name='output_txt' file='parseval_output_test3.txt' lines_diff='8'/>
+            <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
+            <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
+            <param name="delta" value="10"/>
+            <param name="maxtrans" value="10"/>
+            <output name="output_txt" file="parseval_output_test3.txt" lines_diff="8"/>
         </test>
         <test expect_num_outputs="1">
-            <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/>
-            <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/>
-            <param name='output_type' value='html'/>
-            <output name='output_html' file='parseval_output_test4.html' lines_diff='8'/>
+            <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
+            <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
+            <param name="output_type" value="html"/>
+            <output name="output_html" file="parseval_output_test4.html" lines_diff="8"/>
         </test>
         <test expect_num_outputs="1">
-            <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/>
-            <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/>
-            <param name='output_type' value='html'/>
-            <param name='delta' value='10'/>
-            <param name='maxtrans' value='10'/>
-            <output name='output_html' file='parseval_output_test5.html' lines_diff='8'/>
+            <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
+            <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
+            <param name="output_type" value="html"/>
+            <param name="delta" value="10"/>
+            <param name="maxtrans" value="10"/>
+            <output name="output_html" file="parseval_output_test5.html" lines_diff="8"/>
         </test>
         <test expect_num_outputs="1">
-            <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/>
-            <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/>
-            <param name='output_type' value='text'/>
-            <param name='refrlabel' value='example_ref_label'/>
-            <param name='predlabel' value='example_pred_label'/>
-            <output name='output_txt' file='parseval_output_test6.txt' lines_diff='8'/>
+            <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
+            <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
+            <param name="output_type" value="text"/>
+            <param name="refrlabel" value="example_ref_label"/>
+            <param name="predlabel" value="example_pred_label"/>
+            <output name="output_txt" file="parseval_output_test6.txt" lines_diff="8"/>
         </test>
     </tests>
     <help>
@@ -144,5 +144,5 @@
             
 ]]>
     </help>
-    <expand macro='citations'/>
+    <expand macro="citations"/>
 </tool>