diff coverageBed.xml @ 1:82aac94b06c3 draft

Uploaded

--- a/coverageBed.xml	Tue Nov 04 01:45:04 2014 -0500
+++ b/coverageBed.xml	Thu Jan 08 14:25:51 2015 -0500
@@ -6,6 +6,7 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command>
+<![CDATA[
         coverageBed
         #if $inputA.ext == "bam"
             -abam '$inputA'
@@ -18,30 +19,34 @@
         $split
         $strandedness
         | sort -k1,1 -k2,2n
-        &gt; '$output'
+        > '$output'
+]]>
     </command>
     <inputs>
-        <param format="bed,bam,gff,gg3,vcf" name="inputA" type="data" label="Count how many intervals in this BED/VCF/GFF/BAM file (source)">
-            <validator type="unspecified_build" />
-        </param>
-        <param format="bed,gff,gff3,vcf" name="inputB" type="data" label="overlap the intervals in this BED file (target)">
-            <validator type="unspecified_build" />
-        </param>
-        <param name="split" type="boolean" checked="false" truevalue="-split" falsevalue="" label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage"
-            help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data. (-split)" />
+        <param format="bed,bam,gff,gg3,vcf" name="inputA" type="data" label="Count how many intervals in this BED/VCF/GFF/BAM file (source)" />
+        <param format="bed,gff,gff3,vcf" name="inputB" type="data" label="overlap the intervals in this BED file (target)" />
+        <expand macro="split" />
         <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false" 
             help="That is, only features in A are only counted towards coverage in B if they are the same strand. (-s)"/>
-        <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Report the depth at each position in each B feature"
+        <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue=""
+            label="Report the depth at each position in each B feature"
             help="Positions reported are one based.  Each position and depth follow the complete B feature. (-d)" />
-        <param name="hist" type="boolean" checked="false" truevalue="-hist" falsevalue="" label="Report a histogram of coverage for each feature in B as well as a summary histogram for all features in B"
+        <param name="hist" type="boolean" checked="false" truevalue="-hist" falsevalue=""
+            label="Report a histogram of coverage for each feature in B as well as a summary histogram for all features in B"
             help="Additonal columns after each feature in B: 1) depth 2) # bases at depth 3) size of B 4) % of B at depth. (-hist)" />
     </inputs>
-
     <outputs>
-        <data format="bed" name="output" metadata_source="inputB" label="count of overlaps in ${inputA.name} on ${inputB.name}"/>
+        <data format="bed" name="output" metadata_source="inputB" label="Count of overlaps in ${inputA.name} on ${inputB.name}"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="inputA" value="coverageBedA.bed" ftype="bed" />
+            <param name="genome" value="coverageBedB.bed" ftype="bed" />
+            <output name="output" file="coverageBed_result1.bed" ftype="bed" />
+        </test>
+    </tests>
     <help>
-
+<![CDATA[
 **What it does**
 
 coverageBed_ computes both the depth and breadth of coverage of features in 
@@ -58,7 +63,7 @@
 The output file will be comprised of each interval from your original target BED file, plus an additional column indicating the number of intervals in your source file that overlapped that target interval.
 
 @REFERENCES@
-
+]]>
     </help>
     <expand macro="citations" />
 </tool>