diff macros.xml @ 32:b0d5e752c0c5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348

--- a/macros.xml	Fri Aug 18 15:32:52 2017 -0400
+++ b/macros.xml	Tue Sep 05 09:51:56 2017 -0400
@@ -49,10 +49,68 @@
             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. (-split)" />
     </xml>
-    <xml name="genome">
-        <param format="tabular" name="genome" type="data" label="Genome file" />
-        <!--TODO: make use of: ${chromInfo} -->
+    <xml name="input_conditional_genome_file">
+        <conditional name="genome_file_opts">
+            <param name="genome_file_opts_selector" type="select" label="Genome file">
+                <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">
+                    <options from_data_table="__dbkeys__" />
+                </param>
+            </when>
+            <when value="hist">
+                <param name="genome" type="data" format="tabular" label="Genome file" />
+            </when>
+        </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'
+    #end if
+#end if
+    </token>
+    <token name="@GENOME_FILE_MAKEWINDOWS@">
+#if $type.type_select == "genome":
+    #if $type.genome_file_opts.genome_file_opts_selector == "loc":
+        -g '$type.genome_file_opts.genome.fields.len_path'
+    #elif $type.genome_file_opts.genome_file_opts_selector == "hist":
+        -g '$type.genome_file_opts.genome'
+    #end if
+#end if
+    </token>
+    <token name="@GENOME_FILE_UNION@">
+#if $empty.empty_selector == "-empty":
+    #if $empty.genome_file_opts.genome_file_opts_selector == "loc":
+        -g '$empty.genome_file_opts.genome.fields.len_path'
+    #elif $empty.genome_file_opts.genome_file_opts_selector == "hist":
+        -g '$empty.genome_file_opts.genome'
+    #end if
+#end if
+    </token>
+    <token name="@GENOME_FILE_COVERAGE@">
+#if $input_type.input_type_select == "bed":
+    -i '$input_type.input'
+    #if $input_type.genome_file_opts.genome_file_opts_selector == "loc":
+        -g '$input_type.genome_file_opts.genome.fields.len_path'
+    #elif $input_type.genome_file_opts.genome_file_opts_selector == "hist":
+        -g '$input_type.genome_file_opts.genome'
+    #end if
+#elif $input_type.input_type_select == "bam":
+    -ibam '$input_type.input'
+#end if
+    </token>
     <xml name="closest_D_option">
         <param name="iu" type="boolean" checked="false" truevalue="-iu" falsevalue=""
             label="Ignore features in B that are upstream of features in A"