diff build_ceasdb.xml @ 0:4e52505adaa6

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build_ceasdb.xml	Wed Sep 17 15:03:26 2014 -0400
@@ -0,0 +1,65 @@
+<tool name="CEAS: build database" id="ceas_build_db" version="0.1.0">
+  <description>with gene annotation and genome background</description>
+  <macros>
+    <import>ceas_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command interpreter="command">
+  build_genomeBG 
+  #if $ref.refsrc == 'ucsc':
+  -d $ref.dbkey -g $ref.gene_table
+  #elif $ref.refsrc == 'history':
+  -g $ref.gdb
+  #elif $ref.refsrc == 'cached':
+  -g $ref.ceas_db
+  #end if
+  -w $wfile -o $output
+  </command>
+  <inputs>
+    <conditional name="ref">
+      <param name="refsrc" type="select" label="">
+        <option value="ucsc">From UCSC</option>
+        <option value="history">From history</option>
+        <option value="cached">Locally cached CEAS db</option>
+      </param>
+      <when value="ucsc">
+        <param name="dbkey" type="text" value="" label="A UCSC genome id, e.g. mm9">
+        </param>
+        <param name="gene_table" type="text" value="" label="A UCSC gene table name, e.g. refGene">
+        </param>
+      </when>
+      <when value="cached">
+        <param name="ceas_db" type="select" label="">
+          <options from_data_table="ceasdb">
+            <filter type="unique_value" column="0" />
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="gdb" type="data" format="ceasdb" label="Gene annotation table file (sqlite3)">
+        </param>
+      </when>
+    </conditional>
+    <param name="wfile" type="data" format="wig,bigwig"  label="wig / bigwig file">
+      <!-- <validator type="unspecified_build" /> -->
+    </param>
+  </inputs>
+  <outputs>
+   <data format="ceasdb" name="output" label=""/>
+  </outputs>
+ <tests>
+</tests> 
+  <help>
+** CEAS **
+This tool annotates the given intervals and scores with genome
+features such as gene body. It's the major module in CEAS package
+which is written by Hyunjin Gene Shin, published in Bioinformatics
+(pubmed id:19689956).
+
+@EXTERNAL_DOCUMENTATION@
+
+@CITATION_SECTION@
+
+  </help>
+
+</tool>