diff groupbyBed.xml @ 34:dde39ba9c031 draft

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

--- a/groupbyBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/groupbyBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,32 +1,30 @@
-<tool id="bedtools_groupbybed" name="bedtools GroupByBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_groupbybed" name="bedtools GroupByBed" version="@TOOL_VERSION@">
     <description>group by common cols and summarize other cols</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools groupby
-        -i "${inputA}"
-        -g '$group'
-        -c "${cols}"
-        -o $operation
-        > "${output}"
-]]>
-    </command>
+    <command><![CDATA[
+bedtools groupby
+-i '${inputA}'
+-g '$group'
+-c '${cols}'
+-o $operation
+> '${output}'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="inputA" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <expand macro="choose_columns" />
-        <param name="group" type="text" value="1,2,3"
+        <param name="group" argument="-g" type="text" value="1,2,3"
             label="Specifies which column(s) (1-based) should be used to group the input"
-            help="Columns may be comma-separated with each column must be explicitly listed. Or, ranges (e.g. 1-4) are also allowed. (-g)">
+            help="Columns may be comma-separated with each column must be explicitly listed. Or, ranges (e.g. 1-4) are also allowed.">
             <sanitizer invalid_char="">
                 <valid initial="string.digits"><add value=","/><add value="-"/></valid>
             </sanitizer>
         </param>
-        <param name="operation" type="select" label="Specify the operation" help="(-o)">
-            <option value="sum" selected="True">Sum - numeric only</option>
+        <param name="operation" argument="-o" type="select" label="Specify the operation">
+            <option value="sum" selected="true">Sum - numeric only</option>
             <option value="stdev">Stdev - numeric only</option>
             <option value="sstdev">Sstdev - numeric only</option>
             <option value="freqasc">Freqasc - comma separated list of values observed and the number of times they were observed (ascending)</option>
@@ -38,7 +36,7 @@
         </param>
     </inputs>
     <outputs>
-        <data format_source="inputA" name="output" metadata_source="inputA"/>
+        <data name="output" format_source="inputA" metadata_source="inputA"/>
     </outputs>
     <tests>
         <test>
@@ -63,14 +61,12 @@
             <output name="output" file="groupbyBed_result3.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Replicate lines in a file based on columns of comma-separated values.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>