diff coverageBed.xml @ 37:ce3c7f062223 draft

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

--- a/coverageBed.xml	Mon Jun 15 16:55:13 2020 -0400
+++ b/coverageBed.xml	Tue Mar 23 20:23:14 2021 +0000
@@ -24,15 +24,13 @@
 -a '$inputA'
 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
     -b '$reduce_or_iterate.inputB'
-    #if $reduce_or_iterate.inputB.is_of_type('bam'):
-        -sorted -g <(samtools view -H $reduce_or_iterate.inputB | grep '^@SQ' |  sed $'s/\tSN:/\tSN\t/' | sed $'s/\tLN:/\tLN\t/' | cut -f 3,5)
-    #end if
 #else:
     -b
     #for $file in $reduce_or_iterate.inputB
         '$file'
     #end for
 #end if
+@SORTED@
 #if $inputA.is_of_type('gff'):
     | sort -k1,1 -k4,2n
 #else:
@@ -73,6 +71,8 @@
         <param name="a_or_b" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false"
             label="Require that the minimum fraction be satisfied for A OR B."
             help="If -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of  B is covered. Without -e, both fractions would have to be satisfied" />
+        <!-- -sorted -g  -->
+        <expand macro="sorted" />
     </inputs>
     <outputs>
         <data name="output" format="bed" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/>
@@ -86,12 +86,14 @@
         <test>
             <param name="inputA" value="multiCov1.bed" ftype="bed" />
             <param name="inputB" value="srma_in3.bam" ftype="bam" />
+            <param name="sorted" value="true"/>
             <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="multiCov1.bed" ftype="bed" />
             <param name="reduce_or_iterate_selector" value="reduce" />
             <param name="inputB" value="srma_in3.bam" ftype="bam" />
+            <param name="sorted" value="true"/>
             <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
         </test>
         <test>
@@ -107,6 +109,18 @@
             <param name="reciprocal_overlap" value="true"  />
             <output name="output" file="coverageBed_result3_f1r.bed" ftype="bed" />
         </test>
+        <test>
+            <param name="inputA" value="multiCov1.bed" ftype="bed" />
+            <param name="reduce_or_iterate_selector" value="reduce" />
+            <param name="inputB" value="srma_in3.bam,coverageBed.bam" ftype="bam" />
+            <param name="sorted" value="true"/>
+            <output name="output" file="coverageBed_result4_2bam.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="inputA" value="coverageBedA2.bed" ftype="bed" />
+            <param name="inputB" value="coverageBed.bam" ftype="bam" />
+            <output name="output" file="coverageBed_result5_unsorted.bed" ftype="bed" />
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**