diff macros.xml @ 43:07e8b80f278c draft

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

--- a/macros.xml	Wed Jan 12 19:22:14 2022 +0000
+++ b/macros.xml	Fri Apr 01 19:02:51 2022 +0000
@@ -67,48 +67,29 @@
             label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage."
             help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data." />
     </xml>
-    <xml name="input_conditional_genome_file">
+    <xml name="input_conditional_genome_file" token_optional="false" token_help="">
         <conditional name="genome_file_opts">
-            <param name="genome_file_opts_selector" type="select" label="Genome file">
+            <param name="genome_file_opts_selector" type="select" label="Genome file" help="@HELP@">
                 <option value="loc" selected="true">Locally installed Genome file</option>
                 <option value="hist">Genome file from your history</option>
             </param>
             <when value="loc">
-                <param name="genome" type="select" multiple="false" label="Genome file">
+                <param name="genome" type="select" optional="@OPTIONAL@" multiple="false" label="Genome file">
                     <options from_data_table="__dbkeys__" />
                 </param>
             </when>
             <when value="hist">
-                <param name="genome" type="data" format="tabular" label="Genome file" />
+                <param name="genome" type="data" optional="@OPTIONAL@" format="tabular" label="Genome file" />
             </when>
         </conditional>
     </xml>
-    <xml name="input_optional_genome_file">
-        <conditional name="genome">
-            <param name="genome_choose" argument="-g" type="select"
-                label="Specify a genome file that defines the expected chromosome order in the input files." >
-                <option value="" selected="true">No</option>
-                <option value="-g">Yes</option>
-            </param>
-            <when value="-g">
-                <expand macro="input_conditional_genome_file" />
-            </when>
-            <when value="" />
-        </conditional>
-    </xml>
     <token name="@GENOME_FILE@">
-#if $genome_file_opts.genome_file_opts_selector == "loc":
-    '$genome_file_opts.genome.fields.len_path'
-#elif $genome_file_opts.genome_file_opts_selector == "hist":
-    '$genome_file_opts.genome'
-#end if
-    </token>
-    <token name="@GENOME_FILE_MAPBED@">
-#if $genome.genome_choose == "-g":
-    #if $genome.genome_file_opts.genome_file_opts_selector == "loc":
-        -g '$genome.genome_file_opts.genome.fields.len_path'
-    #elif $genome.genome_file_opts.genome_file_opts_selector == "hist":
-        -g '$genome.genome_file_opts.genome'
+#if $genome_file_opts.genome
+    -g 
+    #if $genome_file_opts.genome_file_opts_selector == "loc":
+        '$genome_file_opts.genome.fields.len_path'
+    #elif $genome_file_opts.genome_file_opts_selector == "hist":
+        '$genome_file_opts.genome'
     #end if
 #end if
     </token>