# HG changeset patch
# User greg
# Date 1503576506 14400
# Node ID 5fb237a06499925f5e168cd401488204789880eb
# Parent  0f186cb552c8e184d2eda50b526495a27a89787e
Uploaded

diff -r 0f186cb552c8 -r 5fb237a06499 ideas.xml
--- a/ideas.xml	Thu Aug 24 08:05:46 2017 -0400
+++ b/ideas.xml	Thu Aug 24 08:08:26 2017 -0400
@@ -120,18 +120,36 @@
                 <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>