--- a/ideas.xml	Wed Aug 23 09:20:45 2017 -0400
+++ b/ideas.xml	Wed Aug 23 14:07:10 2017 -0400
@@ -19,10 +19,15 @@
 ## Create the config file and prepare the data
 ##############################################
 #set input_type = $input_type_cond.input_type
-cp '$prep_input_config' 'prep_input_config.txt' &&
 prepMat
 #if str($input_type) == 'datasets':
-    '$prep_input_config'
+    #set cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond
+    #set cell_type_epigenetic_factor = $cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor
+    #if str($cell_type_epigenetic_factor) == 'extract':
+        '$extract_prep_input_config'
+    #else:
+        '$manual_prep_input_config'
+    #end if
     #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
     #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
     #if str($specify_genomic_window) == 'yes':
@@ -51,7 +56,7 @@
 ## Coerce the prepMat config output to the
 ## format expected by the R matrix builder.
 ##############################################
-&& cut -d' ' $prep_input_config -f1,2 > file1.txt
+&& cut -d' ' $manual_prep_input_config -f1,2 > file1.txt
 && ls tmp/*.bed.gz > file2.txt
 && paste <(cat file1.txt) <(cat file2.txt) > $prep_output_config
 ##############################################
@@ -111,9 +116,27 @@
 && mv ./*.state $output_state
     ]]></command>
     <configfiles>
-        <configfile name="prep_input_config"><![CDATA[#for $input_items in $input_type_cond.input_repeat:
+        <configfile name="manual_prep_input_config"><![CDATA[
+#for $input_items in $input_type_cond.input_repeat:
 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input}
-#end for ]]></configfile>
+#end for]]></configfile>
+        <configfile name="extract_prep_input_config"><![CDATA[
+#!/bin/bash
+#set $cell_type_epigenetic_factor_cond=$input_type_cond.cell_type_epigenetic_factor_cond
+#set $input_name_positions=$cell_type_epigenetic_factor_cond.input_name_positions
+#for $i in $cell_type_epigenetic_factor_cond.input:
+    #set $file_path=$i.file_path
+    #set $file_name_with_ext="${file_path##*/}"
+    #set $file_name="${file_name_with_ext%%.*}"
+    #if $input_name_positions == "cell_first":
+        #set $cell_type_name="${file_name%-*}"
+        #set $epigenetic_factor_name="${file_name#*-}"
+    #else:
+        #set $cell_type_name="${file_name#*-}"
+        #set $epigenetic_factor_name="${file_name%-*}"
+    #end if
+${cell_type_name} ${epigenetic_factor_name} ${i}
+#end for]]></configfile>
     </configfiles>
     <inputs>
         <conditional name="input_type_cond">
@@ -122,18 +145,36 @@
                 <option value="data_matrix">Data matrix</option>
             </param>
             <when value="datasets">
-                <repeat name="input_repeat" title="Cell type, Epigenetic factor and Input" min="1">
-                    <param name="cell_type_name" type="text" value="" label="Cell type name">
-                        <validator type="empty_field"/>
+                <conditional name="cell_type_epigenetic_factor_cond">
+                    <param name="cell_type_epigenetic_factor" type="select" label="Set cell type and epigenetic factor names by">
+                        <option value="extract" selected="true">extracting them from the selected input file names</option>
+                        <option value="manual">manually setting them for each selected input</option>
                     </param>
-                    <param name="epigenetic_factor_name" type="text" value="" label="Epigenetic factor name">
-                        <validator type="empty_field"/>
-                    </param>
-                    <param name="input" type="data" format="bigwig,bam" label="BAM or BigWig file">
-                        <validator type="empty_field"/>
-                        <validator type="unspecified_build"/>
-                    </param>
-                </repeat>
+                    <when value="extract">
+                        <param name="input" type="data" format="bigwig,bam" multiple="True" label="BAM or BigWig file">
+                            <validator type="empty_field"/>
+                            <validator type="unspecified_build"/>
+                        </param>
+                        <param name="input_name_positions" type="select" display="radio" label="Selected input file name pattern is" help="A '-' character must separate cell type and epigenetic factor names within the selected input file names">
+                            <option value="cell_first" selected="true">Cell type name - Epigenetic factor name</option>
+                            <option value="cell_last">Epigenetic factor name - Cell type name</option>
+                        </param>
+                    </when>
+                    <when value="manual">
+                        <repeat name="input_repeat" title="Cell type, Epigenetic factor and Input" min="1">
+                            <param name="cell_type_name" type="text" value="" label="Cell type name">
+                                <validator type="empty_field"/>
+                            </param>
+                            <param name="epigenetic_factor_name" type="text" value="" label="Epigenetic factor name">
+                                <validator type="empty_field"/>
+                            </param>
+                            <param name="input" type="data" format="bigwig,bam" label="BAM or BigWig file">
+                                <validator type="empty_field"/>
+                                <validator type="unspecified_build"/>
+                            </param>
+                        </repeat>
+                    </when>
+                </conditional>
                 <conditional name="specify_genomic_window_cond">
                     <param name="specify_genomic_window" type="select" label="Select Bed file that defines genomic windows on which to process the data">
                         <option value="no" selected="true">No</option>