diff ceas_macros.xml @ 0:4e52505adaa6

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ceas_macros.xml	Wed Sep 17 15:03:26 2014 -0400
@@ -0,0 +1,99 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="2014-09-16">cistrome</requirement>
+        </requirements>
+    </xml>
+    <xml name="requirements_bx">
+        <requirements>
+            <requirement type="package" version="2014-09-16">cistrome</requirement>
+            <requirement type="package" version="0.7.1">bx-python</requirement>
+        </requirements>
+    </xml>
+  <xml name="stdio">
+    <stdio>
+        <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />
+        <exit_code range="1:"  level="fatal" description="Error" />
+    </stdio>
+  </xml>
+  <xml name="ceasdb_ref">
+    <conditional name="ref">
+      <param name="refsrc" type="select" label="">
+        <option value="cached">cached</option>
+        <option value="history">history</option>
+        <!--
+        <option value="build">build</option>
+        -->
+      </param>
+      <when value="cached">
+        <param name="ceasdb" 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)"/>
+      </when>
+      <!--
+      <when value="build">
+      </when>
+      -->
+    </conditional>
+  </xml>
+
+  <template name="script_chars">
+#set global $dollar = chr(36)
+#set global $gt = chr(62)
+#set global $lt = chr(60)
+#set global $ad = chr(38)
+  </template>
+
+  <template name="gtpath_ceasdb_ref">
+#if $ref.refsrc == 'history':
+ -g $ref.gdb
+#elif $ref.refsrc == 'cached':
+ -g $ref.ceasdb.fields.path
+## #elif $ref.refsrc == 'build':
+## #else:
+##  -g os.path.join( os.path.abspath($__app__.config.cistrome_static_library_path), "ceaslib", "GeneTable", $dbkey )
+#end if
+  </template>
+  <template name="validate_bedfile_sh">
+##check line count and file format accuracy of bed file
+lines=`wc -l $bfile | tail -1 | awk '{print ${dollar}1}'`
+## bypass validation for now
+## format=`$path/validation/fcfunc.py $bfile`
+format="passed"
+if [[ ${dollar}lines -gt 100000 ]];then
+  echo "BED file is too big! 100K lines are the maximum!" ${gt}${ad}2
+  exit;
+fi
+if [[ ${dollar}format != "passed" ]]; then
+  echo ${dollar}format ${gt}${ad}2
+  exit;
+fi
+  </template>
+
+  <token name="@EXTERNAL_DOCUMENTATION@">
+
+For details about this application, please go to:
+	http://liulab.dfci.harvard.edu/CEAS/usermanual.html
+
+Prebuilt reference Gene annotation tables (SQLite3) are available at:
+	http://liulab.dfci.harvard.edu/CEAS/download.html
+	http://liulab.dfci.harvard.edu/CEAS/src/
+
+Set the dataset datatype to: "ceasdb" when uploading to your history.
+
+  </token>
+  <token name="@CITATION_SECTION@">------
+
+**Citation**
+
+For the underlying tool, please cite the following publication:
+"CEAS: cis-regulatory element annotation system", Hyunjin Shin, Tao Liu, Arjun K. Manrai, and X. Shirley Liu, 
+Bioinformatics. 2009 Oct 1;25(19):2605-6. doi: 10.1093/bioinformatics/btp479. Epub 2009 Aug 18.
+
+  </token>
+</macros>