changeset 11:ac24388a0fda draft

Uploaded

--- a/macs2_callpeak.xml	Thu Jan 23 07:56:46 2014 -0500
+++ b/macs2_callpeak.xml	Thu Jan 23 11:31:32 2014 -0500
@@ -2,6 +2,7 @@
     <description>Call peaks from alignment results</description>
     <expand macro="requirements">
         <requirement type="package" version="3.0.1">R_3_0_1</requirement>
+        <requirement type="set_environment">MACS2_SCRIPT_PATH</requirement>
         <!-- awk and R is missing -->
     </expand>
     <expand macro="version_command" />
@@ -9,6 +10,7 @@
         <import>macs2_macros.xml</import>
     </macros>
     <command>
+        #import os
         #set $temp_stderr = 'macs2_stderr'
         macs2 callpeak
 
@@ -62,10 +64,9 @@
 
         ## TODO
         ## run R to create pdf from model script
-        ##if os.path.exists( os.path.join( tmp_dir, "MACS2_model.r" ) ):
-        ##    cmdline = 'Rscript "MACS2_model.r" > "MACS2_model.r.log"' )
-        ##    proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir )
-        ##    proc.wait()
+        #if os.path.exists( os.getcwd(), "MACS2_model.r" ) ):
+            Rscript "MACS2_model.r" > "MACS2_model.r.log";
+        #end if
 
 
         ## move bed out to proper output file
@@ -89,10 +90,9 @@
         ##parse xls files to interval files as needed
         ##TODO is in working dir
         #if 'peaks_interval' in str($outputs).split(','):
-            #set $file = os.path.join( $tmp_dir, 'MACS2_peaks.xls' )
-            #if os.path.exists( $file ):
+            #if os.path.exists( 'MACS2_peaks.xls' ):
                 echo '#peaks file' > $output_xls_to_interval_peaks_file;
-                awk '$2-=1' $file >> $output_xls_to_interval_peaks_file;
+                awk '$2-=1' MACS2_peaks.xls >> $output_xls_to_interval_peaks_file;
                 ##xls_to_interval( create_peak_xls_file, output_xls_to_interval_peaks_file, header = 'peaks file' )
             #end if
         #end if
@@ -104,7 +104,7 @@
             then 
                 mkdir $output_extra_files.extra_files_path;
                 mv MACS2* $output_extra_files.extra_files_path;
-                python /home/bag/projects/github/galaxytools/macs2/dir2html.py $output_extra_files.extra_files_path $temp_stderr > $output_extra_files;
+                python \$MACS2_SCRIPT_PATH/dir2html.py $output_extra_files.extra_files_path $temp_stderr > $output_extra_files;
             fi;
         #end if
 
@@ -152,6 +152,7 @@
             <option value="gapped">gapped Peaks</option>
             <option value="summits" selected="true">summits</option>
             <option value="peaks_interval">Peaks as interval file</option>
+            <option value="plot">Plot in PDF</option>
             <validator type="no_options" message="Please select at least one output file." />
         </param>
 
@@ -195,6 +196,9 @@
         <data name="output_summits" format="bed" from_work_dir="MACS2_summits.bed" label="${tool.name} on ${on_string} (summits in BED)">
             <filter>'summits' in outputs</filter>
         </data>
+        <data name="output_plot" format="pdf" from_work_dir="MACS2_model.pdf" label="${tool.name} on ${on_string} (plot)">
+            <filter>'pdf' in outputs</filter>
+        </data>
         <data name="output_xls_to_interval_peaks_file" format="interval" label="${tool.name} on ${on_string} (peaks: interval)">
             <filter>'peaks_interval' in outputs</filter>
         </data>

--- a/tool_dependencies.xml	Thu Jan 23 07:56:46 2014 -0500
+++ b/tool_dependencies.xml	Thu Jan 23 11:31:32 2014 -0500
@@ -9,6 +9,9 @@
     <package name="R_3_0_1" version="3.0.1">
         <repository changeset_revision="1d5b86c2e93d" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
+    <set_environment version="1.0">
+        <environment_variable action="set_to" name="MACS2_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
     <package name="macs2" version="2.0.10.2">
         <install version="1.0">
             <actions>