diff sortBed.xml @ 43:07e8b80f278c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"

--- a/sortBed.xml	Wed Jan 12 19:22:14 2022 +0000
+++ b/sortBed.xml	Fri Apr 01 19:02:51 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@" profile="@PROFILE@">
+<tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>order the intervals</description>
     <macros>
         <import>macros.xml</import>
@@ -10,7 +10,7 @@
 sortBed
 -i '$input'
 $option
-@GENOME_FILE_MAPBED@
+@GENOME_FILE@
 > '$output'
     ]]></command>
     <inputs>
@@ -25,7 +25,7 @@
             <option value="-chrThenScoreA">chromosome, then by score (asc).</option>
             <option value="-chrThenScoreD">chromosome, then by score (desc).</option>
         </param>
-        <expand macro="input_optional_genome_file" />
+        <expand macro="input_conditional_genome_file" help="Sort according to the chromosomes declared in a genome file" />
     </inputs>
     <outputs>
         <data name="output" format_source="input" metadata_source="input" label="SortBed on ${input.name}"/>
@@ -44,9 +44,10 @@
         <test>
             <param name="input" value="sortBed2.bed" ftype="bed" />
             <param name="option" value="" />
-            <param name="genome_choose" value="-g" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="mm9.len" ftype="bed" />
+            <conditional name="genome_file_opts">
+                <param name="genome_file_opts_selector" value="hist" />
+                <param name="genome" value="mm9.len" ftype="bed" />
+            </conditional>
             <output name="output" file="sortBed_result3.bed" ftype="bed" />
         </test>
     </tests>