diff intersectBed.xml @ 37:ce3c7f062223 draft

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

--- a/intersectBed.xml	Mon Jun 15 16:55:13 2020 -0400
+++ b/intersectBed.xml	Tue Mar 23 20:23:14 2021 +0000
@@ -16,11 +16,7 @@
 #end if
 
 bedtools intersect
-#if $inputA.is_of_type('bam'):
-    -abam '${inputA}'
-#else:
-    -a '${inputA}'
-#end if
+-a '${inputA}'
 
 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
     -b '$reduce_or_iterate.inputB'
@@ -53,14 +49,7 @@
 $once
 $header
 $modes
-$sorted
-#if str($sorted) != '':
-    #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate' and $reduce_or_iterate.inputB.is_of_type('bam'):
-        -g <(samtools view -H $reduce_or_iterate.inputB | tr ':' '\t' | grep SN | cut -f 3,5)
-    #else if str($reduce_or_iterate.reduce_or_iterate_selector) == 'reduce' and str($reduce_or_iterate.inputB) != 'None' and $reduce_or_iterate.inputB[0].is_of_type('bam'):
-        -g <(samtools view -H $reduce_or_iterate.inputB[0] | tr ':' '\t' | grep SN | cut -f 3,5)
-    #end if
-#end if
+@SORTED@
 $bed
 $count
 > '${output}'
@@ -124,10 +113,9 @@
             help="Reports 0 for A entries that have no overlap with B" />
         <!-- -bed -->
         <param argument="-bed" type="boolean" truevalue="-bed" falsevalue="" checked="false"
-            label="When using BAM input (-abam), write output as BED instead of BAM." />
+            label="When using BAM input, write output as BED instead of BAM." />
         <!-- -sorted -g  -->
-        <param argument="-sorted" type="boolean" truevalue="-sorted" falsevalue="" checked="false"
-            label="For coordinate sorted input file the more efficient sweeping algorithm is enabled." />
+        <expand macro="sorted" />
         <expand macro="print_header" />
     </inputs>
     <outputs>