diff groupbyBed.xml @ 0:b8348686a0b9 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/groupbyBed.xml	Tue Nov 04 01:45:04 2014 -0500
@@ -0,0 +1,44 @@
+<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>
+        bedtools groupby
+        -c $cols
+        -g $group
+        -o $operation
+        -i $inputA
+        &gt; $output
+    </command>
+    <inputs>
+        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
+        <param name="cols" type="text" value="" label="Specify the column(s) (comma separated) that should be summarized" />
+        <param name="group" type="text" value="1,2,3" label="Specifies which column(s) (1-based) should be used to group the input. Columns may be comma-separated with each column must be explicitly listed. Or, ranges (e.g. 1-4) are also allowed." />
+        <param name="operation" 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 - print a comma separated list of values observed and the number of times they were observed. Reported in ascending order of frequency*</option>
+            <option value="freqdesc">Freqdesc - - print a comma separated list of values observed and the number of times they were observed. Reported in descending order of frequency*</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" label=""/>
+    </outputs>
+    <help>
+
+**What it does**
+
+Replicate lines in a file based on columns of comma-separated values.
+
+@REFERENCES@
+    </help>
+    <expand macro="citations" />
+</tool>