# HG changeset patch
# User holtgrewe
# Date 1367858806 14400
# Node ID 08cb79ffac4c82bf92930ce5872a29d11a10ac20
# Parent  0ac4f6f3d984f8fd7f31bbac8f26e87924b4639a
Uploaded

diff -r 0ac4f6f3d984 -r 08cb79ffac4c roi_details.xml
--- a/roi_details.xml	Mon May 06 12:34:43 2013 -0400
+++ b/roi_details.xml	Mon May 06 12:46:46 2013 -0400
@@ -3,6 +3,10 @@
     <description>ROI Details</description>
 
     <command interpreter="python">
+    ln -s ${input} ${input}.${ext}
+
+    ;
+
     roi_details.py --in-file $input --out-file "$out_file" --out-dir "$out_file.files_path"
     #if $max_rois    # --max-rois $max_rois #end if
     #if $link_target # --link-target $link_target #end if
@@ -12,6 +16,10 @@
     #if $ucsc_org    # --ucsc-org $ucsc_org #end if
     #if $ucsc_db     # --ucsc-db $ucsc_db #end if
     #if $ucsc_chr_prefix # --ucsc-chr-prefix "$ucsc_chr_prefix" #end if
+
+    ;
+
+    rm -f ${input} ${input}.${ext}
     </command>
 
     <!--
diff -r 0ac4f6f3d984 -r 08cb79ffac4c roi_plot_thumbnails.xml
--- a/roi_plot_thumbnails.xml	Mon May 06 12:34:43 2013 -0400
+++ b/roi_plot_thumbnails.xml	Mon May 06 12:46:46 2013 -0400
@@ -3,8 +3,12 @@
   <description>Create ROI thumbnail plot grids.</description>
   <!-- First execute HTMl generation (will also create output path), then
        perform PNG creation. -->
-  <command interpreter="python">
-    roi_plot_thumbnails.py --in-file $input --out-file "$out_file" --out-dir "$out_file.files_path"
+  <command>
+    ln -s ${input} ${input}.${input.ext}
+
+    ;
+
+    python roi_plot_thumbnails.py --in-file $input --out-file "$out_file" --out-dir "$out_file.files_path"
     #if $max_rois    # --max-rois $max_rois #end if
     #if $num_rows    # --num-rows $num_rows #end if
     #if $num_cols    # --num-cols $num_cols #end if
@@ -20,13 +24,17 @@
 
     &amp;&amp;
 
-    roi_plot_grid -if $input -o "${out_file.files_path}/roi_plot_grid"
+    roi_plot_thumbnails -if $input -o "${out_file.files_path}/thumbnail_"
     #if $max_rois    # --max-rois $max_rois #end if
     #if $num_rows    # --num-rows $num_rows #end if
     #if $num_cols    # --num-cols $num_cols #end if
     #if $plot_height # --plot-height $plot_height #end if
     #if $plot_width  # --plot-width $plot_width #end if
     #if $max_value   # --max-value $max_value #end if
+
+    ;
+
+    rm -f ${input}.${input.ext}
   </command>
   <inputs>
     <param name="input" format="roi" type="data" label="ROI file to generate statistics for."/>
diff -r 0ac4f6f3d984 -r 08cb79ffac4c roi_report.xml
--- a/roi_report.xml	Mon May 06 12:34:43 2013 -0400
+++ b/roi_report.xml	Mon May 06 12:46:46 2013 -0400
@@ -3,7 +3,15 @@
     <description>ROI Overview Report</description>
 
     <command interpreter="python">
+    ln -s ${input} ${input}.${input.ext}
+
+    ;
+
     roi_report.py --in-file $input --out-file "$out_file" --out-dir "$out_file.files_path"
+
+    ;
+
+    rm -f ${input}.${input.ext}
     </command>
 
     <!--
diff -r 0ac4f6f3d984 -r 08cb79ffac4c roi_table.xml
--- a/roi_table.xml	Mon May 06 12:34:43 2013 -0400
+++ b/roi_table.xml	Mon May 06 12:46:46 2013 -0400
@@ -2,8 +2,12 @@
 <tool id="roi_table" name="ROI Table">
     <description>ROI Overview Report</description>
 
-    <command interpreter="python">
-    roi_table.py --in-file $input --out-file "$out_file" --out-dir "$out_file.files_path"
+    <command>
+    ln -s ${input} ${input}.${input.ext}
+      
+    ;
+
+    python roi_table.py --in-file $input --out-file "$out_file" --out-dir "$out_file.files_path"
     #if $max_rois    # --max-rois $max_rois #end if
     #if $plot_height # --plot-height $plot_height #end if
     #if $plot_width  # --plot-width $plot_width #end if
@@ -14,6 +18,10 @@
     #if $ucsc_org    # --ucsc-org $ucsc_org #end if
     #if $ucsc_db     # --ucsc-db $ucsc_db #end if
     #if $ucsc_chr_prefix # --ucsc-chr-prefix "$ucsc_chr_prefix" #end if
+
+    ;
+
+    rm -f ${input}.${input.ext}
     </command>
 
     <!--