# HG changeset patch
# User Richard Burhans <burhans@bx.psu.edu>
# Date 1334073524 14400
# Node ID 7a94f11fe71f902e3a364d23ed322efe71be135a
# Parent  f810c756a5d62f137c722be96e22db50d8fe303c
change output.extra_files_path to output.files_path

diff -r f810c756a5d6 -r 7a94f11fe71f coverage_distributions.xml
--- a/coverage_distributions.xml	Mon Apr 09 16:51:28 2012 -0400
+++ b/coverage_distributions.xml	Tue Apr 10 11:58:44 2012 -0400
@@ -2,7 +2,7 @@
   <description>distributions</description>
 
   <command interpreter="python">
-    coverage_distributions.py "$input" "0" "$output" "$output.extra_files_path"
+    coverage_distributions.py "$input" "0" "$output" "$output.files_path"
     #if $individuals.choice == '0'
       "all_individuals"
     #else if $individuals.choice == '1'
diff -r f810c756a5d6 -r 7a94f11fe71f dpmix.xml
--- a/dpmix.xml	Mon Apr 09 16:51:28 2012 -0400
+++ b/dpmix.xml	Tue Apr 10 11:58:44 2012 -0400
@@ -2,7 +2,7 @@
   <description>using dynamic programming</description>
 
   <command interpreter="python">
-    dpmix.py "$input" "$data_source" "$switch_penalty" "$ap1_input" "$ap2_input" "$p_input" "$output" "$output2" "$output2.extra_files_path" "$input.dataset.metadata.dbkey" "$input.dataset.metadata.ref" "$GALAXY_DATA_INDEX_DIR" "gd.heterochromatic.loc"
+    dpmix.py "$input" "$data_source" "$switch_penalty" "$ap1_input" "$ap2_input" "$p_input" "$output" "$output2" "$output2.files_path" "$input.dataset.metadata.dbkey" "$input.dataset.metadata.ref" "$GALAXY_DATA_INDEX_DIR" "gd.heterochromatic.loc"
     #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
       #set $arg = '%s:%s' % ($individual_col, $individual)
       "$arg"
diff -r f810c756a5d6 -r 7a94f11fe71f find_intervals.xml
--- a/find_intervals.xml	Mon Apr 09 16:51:28 2012 -0400
+++ b/find_intervals.xml	Tue Apr 10 11:58:44 2012 -0400
@@ -2,7 +2,7 @@
   <description>genomic intervals</description>
 
   <command interpreter="python">
-    find_intervals.py "$input" "$input.metadata.dbkey" "$output" "$output.extra_files_path"
+    find_intervals.py "$input" "$input.metadata.dbkey" "$output" "$output.files_path"
 
     #if $override_metadata.choice == "0"
       "$input.metadata.ref" "$input.metadata.rPos"
diff -r f810c756a5d6 -r 7a94f11fe71f pca.xml
--- a/pca.xml	Mon Apr 09 16:51:28 2012 -0400
+++ b/pca.xml	Tue Apr 10 11:58:44 2012 -0400
@@ -1,7 +1,7 @@
 <tool id="gd_pca" name="PCA" version="1.0.0">
 
   <command interpreter="python">
-    pca.py "$input" "$input.extra_files_path" "$output" "$output.extra_files_path"
+    pca.py "$input" "$input.extra_files_path" "$output" "$output.files_path"
   </command>
 
   <inputs>
diff -r f810c756a5d6 -r 7a94f11fe71f phylogenetic_tree.xml
--- a/phylogenetic_tree.xml	Mon Apr 09 16:51:28 2012 -0400
+++ b/phylogenetic_tree.xml	Tue Apr 10 11:58:44 2012 -0400
@@ -8,7 +8,7 @@
     #else if $individuals.choice == '1'
       "$p1_input"
     #end if
-    "$output" "$output.extra_files_path" "$minimum_coverage" "$minimum_quality"
+    "$output" "$output.files_path" "$minimum_coverage" "$minimum_quality"
 	#if ((str($input.metadata.scaffold) == str($input.metadata.ref)) and (str($input.metadata.pos) == str($input.metadata.rPos))) or (str($include_reference) == '0')
         "none"
     #else
diff -r f810c756a5d6 -r 7a94f11fe71f population_structure.xml
--- a/population_structure.xml	Mon Apr 09 16:51:28 2012 -0400
+++ b/population_structure.xml	Tue Apr 10 11:58:44 2012 -0400
@@ -2,7 +2,7 @@
   <description>structure</description>
 
   <command interpreter="python">
-    population_structure.py "$input" "${input.extra_files_path}/admix.ped" "$output" "$output.extra_files_path" "$populations"
+    population_structure.py "$input" "${input.extra_files_path}/admix.ped" "$output" "$output.files_path" "$populations"
   </command>
 
   <inputs>