changeset 2:438b5c8d736c draft

Deleted selected files

--- a/tabix.xml	Wed Jul 10 15:06:23 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,89 +0,0 @@
-<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>