# HG changeset patch
# User bgruening
# Date 1402590176 14400
# Node ID 295e085b8d605dd2ff3f515f23d8db80d078120f
# Parent  f8111c9f037db39fcd1c709779f5ebccddd1cc76
Uploaded

diff -r f8111c9f037d -r 295e085b8d60 eden_cluster_motif_finder.py
--- a/eden_cluster_motif_finder.py	Thu Jun 12 11:38:08 2014 -0400
+++ b/eden_cluster_motif_finder.py	Thu Jun 12 12:22:56 2014 -0400
@@ -40,8 +40,10 @@
                 motif_count = seq.count(motif)
                 if motif_count > 0:
                     res = '%s\t%s\t%s\t%s\n' % (record.id, motif_id, motif, motif_count)
-                    print res,
-    
+                    args.motif_file.write(res)
+
+    args.motif_file.close()
+
 
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description='Extract motifs patterns with EDeN.')
diff -r f8111c9f037d -r 295e085b8d60 eden_cluster_splitter.pyc
Binary file eden_cluster_splitter.pyc has changed
diff -r f8111c9f037d -r 295e085b8d60 eden_iterative_motif_finder.pyc
Binary file eden_iterative_motif_finder.pyc has changed
diff -r f8111c9f037d -r 295e085b8d60 eden_utilities.py
--- a/eden_utilities.py	Thu Jun 12 11:38:08 2014 -0400
+++ b/eden_utilities.py	Thu Jun 12 12:22:56 2014 -0400
@@ -59,7 +59,7 @@
             dest="fraction_center_scan",
             type=int, 
             help='Fraction of total number of instances which is used to compute densities.', 
-            default=1.0)
+            default=1)
         
     if mode == 'eden_iterative_motif_finder' or  mode == 'eden_cluster_motif' :
         parser.add_argument("-f", "--output-file", 
@@ -83,4 +83,10 @@
             help='Number of negative instances per order per positive instance.', 
             default=3)
 
-    return parser
\ No newline at end of file
+    if mode == 'eden_cluster_motif' :
+        parser.add_argument("--motif-file", 
+            dest="motif_file", 
+            type=argparse.FileType('w'),
+            default=sys.stdout,
+            help="Path to the output motif file.")
+    return parser
diff -r f8111c9f037d -r 295e085b8d60 eden_utilities.pyc
Binary file eden_utilities.pyc has changed
diff -r f8111c9f037d -r 295e085b8d60 eden_wrapper.pyc
Binary file eden_wrapper.pyc has changed
diff -r f8111c9f037d -r 295e085b8d60 motif_finder.xml
--- a/motif_finder.xml	Thu Jun 12 11:38:08 2014 -0400
+++ b/motif_finder.xml	Thu Jun 12 12:22:56 2014 -0400
@@ -2,7 +2,7 @@
     <description>based on EDeN</description>
     <requirements>
         <requirement type="package" version="1.63">biopython</requirement>
-        <requirement type="package" version="1.3.5">eden</requirement>
+        <requirement type="package" version="10">eden</requirement>
     </requirements>
     <command interpreter="python">
         eden_cluster_motif_finder.py
@@ -10,7 +10,7 @@
         --input-file $infile
         --radius $radius
         --distance $distance
-        --output-dir ./
+        --output-dir "./foo"
         --num-nearest-neighbors $num_nearest_neighbors
         --neighborhood-intersection-size $neighborhood_intersection_size
         --fraction-center-scan $fraction_center_scan
@@ -18,7 +18,7 @@
         --max-order $max_order
         --min-motif-size $min_motif_size
         --num-negative-repetitions $num_negative_repetitions
-        > $output
+        --motif-file $output
     </command>
     <inputs>
         <param name="infile" type="data" format="fasta" label="sequences" help="in FASTA format (--input-file)"/>
@@ -27,7 +27,7 @@
         <param name="num_nearest_neighbors" type="integer" value="10" label="Number of nearest neighbors used in the density estimation" help="(--num-nearest-neighbors)" />
         <param name="neighborhood_intersection_size" type="integer" value="5" label="Number of nearest neighbors that must be shared in neighborhood in order to trigger neighborhood joining."
             help="(--neighborhood-intersection-size)" />
-        <param name="fraction_center_scan" type="float" value="1.0" label="Fraction of total number of instances which is used to compute densities" help="(--fraction-center-scan)" />
+        <param name="fraction_center_scan" type="integer" value="1" label="Fraction of total number of instances which is used to compute densities" help="(--fraction-center-scan)" />
         <param name="max_order" type="integer" value="3" label="Size of the order for negative shuffling" help="(--max_order)" />
         <param name="min_motif_size" type="integer" value="4" label="Size of the smallest returned motif" help="(--min-motif-size)" />
         <param name="num_negative_repetitions" type="integer" value="3" label="Size of the smallest returned motif" help="(--num-negative-repetitions)" />
diff -r f8111c9f037d -r 295e085b8d60 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jun 12 11:38:08 2014 -0400
+++ b/tool_dependencies.xml	Thu Jun 12 12:22:56 2014 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="eden" version="1.3.5">
-        <repository changeset_revision="dc13e98b0e3d" name="package_eden_1_3" owner="rnateam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="eden" version="10">
+        <repository changeset_revision="d1fd8665ea78" name="package_eden_latest" owner="bgruening" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="biopython" version="1.63">
         <repository changeset_revision="d8b200f1f5a5" name="package_biopython_1_63" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" />