# HG changeset patch
# User pjbriggs
# Date 1429628207 14400
# Node ID 695d61decd06afcb9ce14a4db4c8606608f53c91
# Parent  d9032bb158b9c3eed6e3c5e011883bc5c2224d1a
Make dependency on R explicit.

diff -r d9032bb158b9 -r 695d61decd06 ceasbw_wrapper.sh
--- a/ceasbw_wrapper.sh	Wed Jan 28 05:04:46 2015 -0500
+++ b/ceasbw_wrapper.sh	Tue Apr 21 10:56:47 2015 -0400
@@ -20,6 +20,13 @@
     if [ "$7" == "--bigwig" ] ; then
 	CEAS=ceasBW
     fi
+    if [ "$7" == "--length" ] ; then
+	chrom_sizes=$8
+	if [ ! -f "$chrom_sizes" ] ; then
+	    echo "ERROR no file $chrom_sizes, stopping" >&2
+	    exit 1
+	fi
+    fi
     OPTIONS="$OPTIONS $7"
     shift
 done
diff -r d9032bb158b9 -r 695d61decd06 ceasbw_wrapper.xml
--- a/ceasbw_wrapper.xml	Wed Jan 28 05:04:46 2015 -0500
+++ b/ceasbw_wrapper.xml	Tue Apr 21 10:56:47 2015 -0400
@@ -1,4 +1,10 @@
 <tool id="ceasbw" name="CEAS" version="1.0.2-0">
+  <requirements>
+    <requirement type="package" version="1.2.5">python_mysqldb</requirement>
+    <requirement type="package" version="0.7.1">bx_python</requirement>
+    <requirement type="package" version="1.0.2.d8c0751">cistrome_ceas</requirement>
+    <requirement type="package" version="3.1.2">R</requirement>
+  </requirements>
   <description>Annotate intervals and scores with genome features (cistrome CEAS)</description>
   <command interpreter="bash">ceasbw_wrapper.sh $bed_file $gdb_file $extra_bed_file $log_output $pdf_report $xls_output
   #if (str($wig_file.ext) == 'bigwig')
@@ -14,11 +20,6 @@
   --bisizes $bisizes_lower,$bisizes_upper
   --pf-res $profiling_resolution
   --rel-dist $relative_distance</command>
-  <requirements>
-    <requirement type="package" version="1.2.5">python_mysqldb</requirement>
-    <requirement type="package" version="0.7.1">bx_python</requirement>
-    <requirement type="package" version="1.0.2.d8c0751">cistrome_ceas</requirement>
-  </requirements>
   <inputs>
     <param name="bed_file" type="data" format="bed" label="BED file with ChIP regions" />
     <param name="wig_file" type="data" format="wig,bigwig" label="WIG or BIGWIG file for wig profiling or genome background annotation" optional="true" />
diff -r d9032bb158b9 -r 695d61decd06 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jan 28 05:04:46 2015 -0500
+++ b/tool_dependencies.xml	Tue Apr 21 10:56:47 2015 -0400
@@ -1,5 +1,10 @@
 <?xml version="1.0"?>
 <tool_dependency>
+  <!-- Dependencies from main/test toolsheds -->
+  <package name="R" version="3.1.2">
+    <repository changeset_revision="41f43a2064ba" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+  </package>
+  <!-- Python mysqldb package -->
   <package name="python_mysqldb" version="1.2.5">
     <install version="1.0">
       <actions>