diff tagBed.xml @ 34:dde39ba9c031 draft

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

--- a/tagBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/tagBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,38 +1,38 @@
-<tool id="bedtools_tagbed" name="bedtools TagBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_tagbed" name="bedtools TagBed" version="@TOOL_VERSION@+galaxy1">
     <description>tag BAM alignments based on overlaps with interval files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        #set files = '" "'.join( [ str( $file ) for $file in $inputB ] )
-        bedtools tag
-        -i "${inputA}"
-        -files "${files}"
-        -f $overlap
-        $strand
-        -tag "${tag}"
-        $field
-        > "${output}"
-]]>
-    </command>
+    <command><![CDATA[
+bedtools tag
+-i '${inputA}'
+-files
+#for $file in $inputB
+    '$file'
+#end for
+@OVERLAP@
+$strand
+-tag '${tag}'
+$field
+> '${output}'
+    ]]></command>
     <inputs>
-        <param name="inputA" format="bam" type="data" label="BAM file"/>
-        <param name="inputB" format="@STD_BEDTOOLS_INPUTS@" multiple="True" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
+        <param name="inputA" argument="-i" type="data" format="bam" label="BAM file"/>
+        <param name="inputB" argument="-files" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
         <expand macro="strand2" />
-        <expand macro="overlap" />
-        <param name="tag" type="text" value="YB" label="Specify the tag to use" />
+        <expand macro="overlap" fracof="the alignment"/>
+        <param argument="-tag" type="text" value="YB" label="Specify the tag to use" />
         <param name="field" type="select" label="Field from the annotation files to populate tags?">
-            <option value="-labels" selected="True">Labels</option>
+            <option value="-labels" selected="true">Labels</option>
             <option value="-scores">Scores</option>
             <option value="-names">Names</option>
             <option value="-labels -intervals">Intervals</option>
         </param>
     </inputs>
     <outputs>
-        <data format="bam" name="output"/>
+        <data name="output" format="bam" />
     </outputs>
     <tests>
         <test>
@@ -42,14 +42,12 @@
             <output name="output" file="tagBed_result1.bam" ftype="bam" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Annotates a BAM file based on overlaps with multiple @STD_BEDTOOLS_INPUT_LABEL@ files on the intervals in an input bam file
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>