# HG changeset patch
# User greg
# Date 1511364244 18000
# Node ID d064db60a06de4a54690998d0ee4c02cbd052bb5
# Parent  de93d8e8a09637746c4aa65091534fa50c8291b1
Uploaded

diff -r de93d8e8a096 -r d064db60a06d ideas.xml
--- a/ideas.xml	Wed Nov 22 08:37:10 2017 -0500
+++ b/ideas.xml	Wed Nov 22 10:24:04 2017 -0500
@@ -9,7 +9,6 @@
         <requirement type="package" version="1.4.4">r-optparse</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-#set window_positions_by_chrom = "window.inv"
 #set output_pdf_dir = "output_pdf_dir"
 #set output_txt_dir = "output_txt_dir"
 #set tmp_dir = "tmp"
@@ -26,8 +25,6 @@
 $prep_input_config
 #if str($specify_genomic_window) == "yes":
     -bed '$specify_genomic_window_cond.bed_input'
-    #import collections
-    chroms = collections.OrderedDict()
 #else:
     -gsz '$chromInfo'
     -wsz $specify_genomic_window_cond.window_size
@@ -60,45 +57,110 @@
 ## the IDEAS -inv option.
 ##############################################
 #if str($specify_genomic_window) == "yes":
-    $categorize_window_positions_by_chrom
-    #for chrom, tup in $chroms.items():
+    #import collections
+    #set window_positions_by_chroms = collections.OrderedDict()
+    #for count, line in enumerate(open($specify_genomic_window_cond.bed_input.file_name, 'r')):
+        #set $line = $line.strip()
+        #if not $line or $line.startswith('#'):
+            #continue
+        #end if
+        #set items = $line.split('\t')
+        #if $items[0] in $window_positions_by_chroms:
+            #set tup = $window_positions_by_chroms[$items[0]]
+            #set $tup[1] += 1
+            #set $window_positions_by_chroms[$items[0]] = $tup
+        #else:
+            #set $window_positions_by_chroms[$items[0]] = [$count, $count+1]
+        #end if
+    #end for
+    #for chrom, tup in $window_positions_by_chroms.items():
         && ideas
         '$prep_output_config'
-        $ideas_options
+        '$specify_genomic_window_cond.bed_input'
+        $hp
+        -inv $tup[0] $tup[1]
+        #if str($log2) != "0.0":
+            -log2 $log2
+        #end if
+        #if str($max_states) != "0.0":
+            -G $max_states
+        #end if
+        #if str($initial_states) != "0":
+            -C $initial_states
+        #end if
+        #if str($max_position_classes) != "0":
+            -P $max_position_classes
+        #end if
+        #if str($max_cell_type_clusters) != "0":
+            -K $max_cell_type_clusters
+        #end if
+        #if str($prior_concentration) != "0.0":
+            -A $prior_concentration
+        #end if
+        -sample $burnin_num $mcmc_num
+        #if str($minerr) != "0.0":
+            -minerr $minerr
+        #end if
+        #if str($maxerr) != "0.0":
+            -maxerr $maxerr
+        #end if
+        -rseed $rseed
+        -thread \${GALAXY_SLOTS:-4}
+        -o '$project_name.$chrom'
+        #if str($save_ideas_log) == "yes":
+            >> $output_log
+        #else:
+            > /dev/null
+        #end if
     #end for
 #else:
     && ideas
     '$prep_output_config'
-    $ideas_options
-    && mv ./*.cluster '$output_txt_dir'
-    && mv ./*.para '$output_txt_dir'
-    && mv ./*.profile '$output_txt_dir'
-    && mv ./*.state '$output_txt_dir'
+    $tmp_dir/*.bed
+    $hp
+    #if str($log2) != "0.0":
+        -log2 $log2
+    #end if
+    #if str($max_states) != "0.0":
+        -G $max_states
+    #end if
+    #if str($initial_states) != "0":
+        -C $initial_states
+    #end if
+    #if str($max_position_classes) != "0":
+        -P $max_position_classes
+    #end if
+    #if str($max_cell_type_clusters) != "0":
+        -K $max_cell_type_clusters
+    #end if
+    #if str($prior_concentration) != "0.0":
+        -A $prior_concentration
+    #end if
+    -sample $burnin_num $mcmc_num
+    #if str($minerr) != "0.0":
+        -minerr $minerr
+    #end if
+    #if str($maxerr) != "0.0":
+        -maxerr $maxerr
+    #end if
+    -rseed $rseed
+    -thread \${GALAXY_SLOTS:-4}
     -o '$project_name'
     #if str($save_ideas_log) == "yes":
         > $output_log
     #else:
         > /dev/null
     #end if
-    && Rscript '$__tool_directory__/create_heatmap.R'
-    -i '$output_txt_dir'
-    -o '$output_pdf_dir'
 #end if
+&& mv ./*.cluster '$output_txt_dir'
+&& mv ./*.para '$output_txt_dir'
+&& mv ./*.profile '$output_txt_dir'
+&& mv ./*.state '$output_txt_dir'
+&& Rscript '$__tool_directory__/create_heatmap.R'
+-i '$output_txt_dir'
+-o '$output_pdf_dir'
     ]]></command>
     <configfiles>
-        <configfile name="categorize_window_positions_by_chrom"><![CDATA[#with #open($specify_genomic_window_cond.bed_input, 'r') as fh:
-    #for count, line in enumerate($fh):
-        $line = $line.strip()
-        #if not $line or $line.startswith('#'):
-            #continue
-        items = $line.split('\t')
-        chrom = $items[0]
-        #if $chrom in $chroms:
-            tup = $chroms[$chrom]
-            $tup[1] += 1
-            $chroms[$chrom] = $tup
-        else:
-            $chroms[$chrom] = [$count, $count+1]]]></configfile>
         <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
     #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions
     #for $i in $cell_type_epigenetic_factor_cond.input:
@@ -119,39 +181,6 @@
 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input}
     #end for
 #end if]]></configfile>
-        <configfile name="ideas_options"><![CDATA[#if str($specify_genomic_window) == "yes":
-    '$specify_genomic_window_cond.bed_input'
-#else:
-    $tmp_dir/*.bed
-#end if
-$hp
-#if str($log2) != "0.0":
-    -log2 $log2
-#end if
-#if str($max_states) != "0.0":
-    -G $max_states
-#end if
-#if str($initial_states) != "0":
-    -C $initial_states
-#end if
-#if str($max_position_classes) != "0":
-    -P $max_position_classes
-#end if
-#if str($max_cell_type_clusters) != "0":
-    -K $max_cell_type_clusters
-#end if
-#if str($prior_concentration) != "0.0":
-    -A $prior_concentration
-#end if
--sample $burnin_num $mcmc_num
-#if str($minerr) != "0.0":
-    -minerr $minerr
-#end if
-#if str($maxerr) != "0.0":
-    -maxerr $maxerr
-#end if
--rseed $rseed
--thread \${GALAXY_SLOTS:-4}]]></configfile>
     </configfiles>
     <inputs>
         <conditional name="cell_type_epigenetic_factor_cond">
@@ -368,4 +397,4 @@
     <citations>
         <citation type="doi">10.1093/nar/gkw278</citation>
     </citations>
-</tool>
+</tool>
\ No newline at end of file