diff jaccardBed.xml @ 34:dde39ba9c031 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95

--- a/jaccardBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/jaccardBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,35 +1,37 @@
-<tool id="bedtools_jaccard" name="bedtools JaccardBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_jaccard" name="bedtools JaccardBed" version="@TOOL_VERSION@+galaxy1">
     <description>calculate the distribution of relative distances between two files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools jaccard
-            $strand
-            $split
-            $reciprocal
-            -f $overlap
-            -a '$inputA'
-            -b '$inputB'
-            > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools jaccard
+$strand
+$split
+$reciprocal
+@OVERLAP@
+#if str($overlapB):
+   -F $overlapB
+#end if
+-a '$inputA'
+-b '$inputB'
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <expand macro="overlap" />
+        <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/>
         <expand macro="reciprocal" />
-        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
+        <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
             label="Force strandedness"
-            help="That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand. (-s)" />
+            help="That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand." />
         <expand macro="strand2" />
         <expand macro="split" />
     </inputs>
     <outputs>
-        <data format_source="inputA" name="output" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}" />
+        <data name="output" format_source="inputA" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}" />
     </outputs>
     <tests>
         <test>
@@ -44,8 +46,7 @@
             <output name="output" file="jaccardBed_result2.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-
+    <help><![CDATA[
 **What it does**
 
 By default, bedtools jaccard reports the length of the intersection, the length of the union (minus the intersection), the final Jaccard statistic reflecting the similarity of the two sets, as well as the number of intersections.
@@ -58,6 +59,6 @@
 The jaccard tool requires that your data is pre-sorted by chromosome and then by start position (e.g., sort -k1,1 -k2,2n in.bed > in.sorted.bed for BED files).
 
 @REFERENCES@
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>