changeset 1:eb790a7f5e7a draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tabix.xml	Wed Jul 10 15:06:23 2013 -0400
@@ -0,0 +1,89 @@
+<tool id="tabix" name="tabix" version="0.0.1">
+    <description>Generic indexer for TAB-delimited genome position files.</description>
+    <requirements>
+        <requirements type="package" version= "0.2.6">tabix</requirements>
+    </requirements>
+    <command>
+        tabix
+    #if str($position) == "no"
+        -0
+    #end if
+
+    #if str($options.extension) == "tabular"
+        #if str($options.columnseq) != ""
+            -s $options.columnseq
+        #end if
+
+        #if str($options.columnstart) != ""
+            -b $options.columnstart 
+        #end if
+
+        #if str($options.columnend) != ""
+            -e $options.columnend
+        #end if
+
+        #if str($options.skiplines) != ""
+            -S $options.skiplines
+        #end if
+
+        #if str($options.skipchar) != ""
+            -c $options.skipchar
+        #end if
+    #else
+        -p
+    #end if
+
+    $input $region
+    
+    </command>
+    <inputs>
+        <param name="input" type="data" label="Input file" format="gff,bed,sam,vcf,tabular">
+             </param>
+        <param name="region" type="text" optional="true" label="Regions (seperate with spaces)"> </param>
+        <conditional name="optional">
+            <param name= "extension" type="select" value= "tabular" label= "Input Extension"> 
+                <option value="tabular">tabular</option>
+                <option value="gff">gff</option>
+                <option value="bed">bed</option>
+                <option value="sam">sam</option>
+                <option value="vcf">vcf</option>
+            </param>       
+            <when value="tabular">
+                     <param name="columnseq" type="integer" optional= "true" label="Column of sequence name" />
+                     <param name="columnstart" type="integer" optional= "true" label="Column of start chromosomal position" />
+                     <param name="columnend" type="integer" optional= "true" label="Column of end chromosomal position" />
+                     <param name="skiplines" type="integer" optional= "true" label="Skip first INT lines" />
+                     <param name="skipchar" type="text" optional= "true" label="Skip lines started with CHAR" />
+                     <param name="position" type= "select" value= "yes" label="1-based? (if not, 0-based)">
+                        <option value= "yes">yes</option>
+                        <option value= "no">no</option>
+                    </param>
+                </when>   
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <data format="tabular" name="output" />
+    </outputs>
+
+    <help>
+**What it does:** 
+
+Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file in.tab.bgz.tbi when region is absent from the command-line. The input data file must be position sorted and compressed by bgzip which has a gzip(1) like interface. After indexing, tabix is able to quickly retrieve data lines overlapping regions specified in the format "chr:beginPos-endPos". Fast data retrieval also works over network if URI is given as a file name and in this case the index file will be downloaded if it is not present locally.
+
+**Citation:**
+
+Tabix was written by Heng Li. The BGZF library was originally implemented by Bob Handsaker and modified by Heng Li for remote file access and in-memory caching.
+
+http://samtools.sourceforge.net/tabix.shtml
+
+**Example:**
+
+(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz;
+
+tabix -p gff sorted.gff.gz;
+
+tabix sorted.gff.gz chr1:10,000,000-20,000,000;
+
+    </help>
+</tool>