diff genomeCoverageBed.xml @ 17:44867b59dbf2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174

--- a/genomeCoverageBed.xml	Fri Aug 18 15:33:08 2017 -0400
+++ b/genomeCoverageBed.xml	Tue Sep 05 15:40:14 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_genomecoveragebed" name="Genome Coverage" version="@WRAPPER_VERSION@.0">
+<tool id="bedtools_genomecoveragebed" name="Genome Coverage" version="@WRAPPER_VERSION@.1">
     <description>compute the coverage over an entire genome</description>
     <macros>
         <import>macros.xml</import>
@@ -8,12 +8,7 @@
     <command>
 <![CDATA[
         bedtools genomecov
-        #if $input_type.input_type_select == 'bam'
-            -ibam '$input_type.input'
-        #else
-            -i '$input_type.input'
-            -g '$input_type.genome'
-        #end if
+        @GENOME_FILE_COVERAGE@
 
         $split
         $strand
@@ -49,7 +44,7 @@
             </param>
             <when value="bed">
                 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file" />
-                <expand macro="genome" />
+                <expand macro="input_conditional_genome_file" />
             </when>
             <when value="bam">
                 <param format="bam" name="input" type="data" label="BAM file" />
@@ -65,11 +60,11 @@
                     label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported.  (-bga)" />
                 <param name="scale" type="float" value="1.0"
                     label="Scale the coverage by a constant factor"
-                    help="Each bedGraph coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM). (-scale)"/>
+                    help="Each bedGraph coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM). (-scale)" />
             </when>
             <when value="hist">
                 <param name="max" type="integer" label="Specify max depth" value="0"
-                    help="Combine all positions with a depth >= max into a single bin in the histogram. (-max)"/>
+                    help="Combine all positions with a depth >= max into a single bin in the histogram. (-max)" />
             </when>
         </conditional>
         <expand macro="split" />
@@ -99,6 +94,7 @@
         <test>
             <param name="input_type_select" value="bed" />
             <param name="input" value="genomeCoverageBed1.bed" ftype="bed" />
+            <param name="genome_file_opts_selector" value="hist" />
             <param name="genome" value="genomeCoverageBed1.len" ftype="tabular" />
             <param name="report_select" value="hist" />
             <output name="output" file="genomeCoverageBed_result1.bed" ftype="tabular" />