diff mergeBed.xml @ 2:457b09031d57 draft

Uploaded

--- a/mergeBed.xml	Thu Jan 08 14:25:51 2015 -0500
+++ b/mergeBed.xml	Tue May 19 07:05:36 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_mergebed" name="Merge BED files" version="@WRAPPER_VERSION@.0">
+<tool id="bedtools_mergebed" name="Merge BED files" version="@WRAPPER_VERSION@.1">
     <description>(mergeBed)</description>
     <macros>
         <import>macros.xml</import>
@@ -12,6 +12,7 @@
             $strand
             -d $distance
             $header
+            @C_AND_O_ARGUMENT@
             > "${output}"
 ]]>
     </command>
@@ -27,11 +28,7 @@
             label="Maximum distance between features allowed for features to be merged"
             help="That is, overlapping and/or book-ended features are merged. (-d)"/>
         <expand macro="print_header" />
-        <expand macro="choose_columns" />
-        <expand macro="choose_operations">
-            <expand macro="math_options" />
-            <expand macro="additional_math_options" />
-        </expand>
+        <expand macro="c_and_o_argument" />
     </inputs>
     <outputs>
         <data format="bed" name="output" metadata_source="input" label="Merged ${input.name}"/>
@@ -56,6 +53,15 @@
             <param name="distance" value="1000" />
             <output name="output" file="mergedBed_result4.bed" ftype="bed" />
         </test>
+        <test>
+            <param name="input" value="mergedBed4.bed" ftype="bed" />
+            <param name="distance" value="1000" />
+            <repeat name="c_and_o_argument_repeat">
+                <param name="col" value="1"/>
+                <param name="operation" value="count"/>
+            </repeat>
+            <output name="output" file="mergedBed_result5.bed" ftype="bed" />
+        </test>
     </tests>
     <help>
 <![CDATA[
@@ -92,7 +98,7 @@
 
 
 ==========================================================================
-*-s* Enforcing "strandedness" 
+*-s* Enforcing "strandedness"
 ==========================================================================
 The ``-s`` option will only merge intervals that are overlapping/bookended
 *and* are on the same strand.
@@ -112,26 +118,6 @@
 
 
 ==========================================================================
-*-n* Reporting the number of features that were merged 
-==========================================================================
-The -n option will report the number of features that were combined from the 
-original file in order to make the newly merged feature. If a feature in the 
-original file was not merged with any other features, a "1" is reported.
-
-::
-
-  $ cat A.bed
-  chr1  100  200
-  chr1  180  250
-  chr1  250  500
-  chr1  501  1000
-  
-  $ bedtools merge -i A.bed -n
-  chr1  100  500  3
-  chr1  501  1000 1
-
-
-==========================================================================
 *-d* Controlling how close two features must be in order to merge 
 ==========================================================================
 By default, only overlapping or book-ended features are combined into a new 
@@ -154,48 +140,6 @@
   chr1  100  200  1000
 
 
-=============================================================
-*-nms* Reporting the names of the features that were merged
-=============================================================
-Occasionally, one might like to know that names of the features that were 
-merged into a new feature. The ``-nms`` option will add an extra column to the 
-``merge`` output which lists (separated by semicolons) the names of the
-merged features.
-
-::
-
-  $ cat A.bed
-  chr1  100  200  A1
-  chr1  150  300  A2
-  chr1  250  500  A3
- 
-  $ bedtools merge -i A.bed -nms
-  chr1  100  500  A1,A2,A3
-  
-
-===============================================================
-*-scores* Reporting the scores of the features that were merged
-===============================================================
-Similarly, we might like to know that scores of the features that were 
-merged into a new feature. Enter the ``-scores`` option.  One can specify 
-how the scores from each overlapping interval should be reported.
-
-::
-
-  $ cat A.bed
-  chr1  100  200  A1 1
-  chr1  150  300  A2 2
-  chr1  250  500  A3 3
- 
-  $ bedtools merge -i A.bed -scores mean
-  chr1  100  500  2
-  
-  $ bedtools merge -i A.bed -scores max
-  chr1  100  500  3
-
-  $ bedtools merge -i A.bed -scores collapse
-  chr1  100  500  1,2,3
-
 @REFERENCES@
 ]]>
     </help>