diff sortBed.xml @ 54:b06c53665eb6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"

--- a/sortBed.xml	Mon Jun 15 20:49:30 2020 +0000
+++ b/sortBed.xml	Tue Mar 23 20:21:30 2021 +0000
@@ -9,6 +9,7 @@
 sortBed
 -i '$input'
 $option
+@GENOME_FILE_MAPBED@
 > '$output'
     ]]></command>
     <inputs>
@@ -23,6 +24,7 @@
             <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" />
     </inputs>
     <outputs>
         <data name="output" format_source="input" metadata_source="input" label="SortBed on ${input.name}"/>
@@ -33,6 +35,19 @@
             <param name="option" value="" />
             <output name="output" file="sortBed_result1.bed" ftype="bed" />
         </test>
+        <test>
+            <param name="input" value="sortBed2.bed" ftype="bed" />
+            <param name="option" value="" />
+            <output name="output" file="sortBed_result2.bed" ftype="bed" />
+        </test>
+        <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" />
+            <output name="output" file="sortBed_result3.bed" ftype="bed" />
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**