diff groupbyBed.xml @ 8:0d3aa592ce27 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/groupbyBed.xml	Tue Apr 28 22:56:34 2015 -0400
@@ -0,0 +1,76 @@
+<tool id="bedtools_groupbybed" name="GroupByBed" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+<![CDATA[
+        bedtools groupby
+        -c "${cols}"
+        -g $group
+        -o $operation
+        -i "${inputA}"
+        > "${output}"
+]]>
+    </command>
+    <inputs>
+        <param format="bed" name="inputA" type="data" label="BED file"/>
+        <expand macro="choose_columns" />
+        <param name="group" 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)">
+            <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>
+            <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>
+            <option value="freqdesc">Freqdesc - comma separated list of values observed and the number of times they were observed (descending)</option>
+            <option value="first">First - numeric or text</option>
+            <option value="last">Last - numeric or text</option>
+            <expand macro="math_options" />
+            <expand macro="additional_math_options" />
+        </param>
+    </inputs>
+    <outputs>
+        <data format_source="inputA" name="output" metadata_source="inputA"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputA" value="groupbyBed1.bed" ftype="bed" />
+            <param name="cols" value="9" />
+            <param name="group" value="1,2,3" />
+            <param name="operation" value="sum" />
+            <output name="output" file="groupbyBed_result1.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="inputA" value="groupbyBed1.bed" ftype="bed" />
+            <param name="cols" value="9" />
+            <param name="group" value="1,2,3" />
+            <param name="operation" value="min" />
+            <output name="output" file="groupbyBed_result2.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="inputA" value="groupbyBed1.bed" ftype="bed" />
+            <param name="cols" value="9" />
+            <param name="group" value="1-4" />
+            <param name="operation" value="median" />
+            <output name="output" file="groupbyBed_result3.bed" ftype="bed" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+Replicate lines in a file based on columns of comma-separated values.
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>