remove section and better handle different outputs

src/galaxy/je-demultiplex-illu.xml

@@ -95,7 +95,8 @@
             <param name="MMD" value="2"/>
             <param name="Q" value="20"/>
 	        <param name="DIAG" value="false"/>
-            <output name="METRICS_FILE_NAME" file="illu_summary_PE.txt" ftype="tabular" lines_diff="4">
+            <output name="METRICS_FILE_NAME" file="illu_summary_PE.txt" ftype="tabular" lines_diff="4"/>
+            <output name="DEMULTIPLEX_RESULTS" ftype="tabular">
                 <discovered_dataset designation="unassigned_1" file="illu_unassigned_1_PE.txt" />
                 <discovered_dataset designation="unassigned_2" file="illu_unassigned_2_PE.txt" />
                 <discovered_dataset designation="emb681m5_GGACTCCTCTCTCTAT_2" file="emb681m5_GGACTCCTCTCTCTAT_2.txt"/>
@@ -123,6 +124,7 @@ Input files are fastq files, and can be in gzip compressed format.
 Author: Charles Girardot  (charles.girardot@embl.de).
 
 Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
+With contributions by: Mehmet Tekman (@mtekman)
 
 ------
 

src/galaxy/je-demultiplex.xml

@@ -60,7 +60,8 @@
             <param name="type" value="single"/>
             <param name="input_1" value="file_1_sequence.txt" ftype="fastqsanger"/>
             <param name="BARCODE_FILE" value="barcodes_SE.txt" ftype="tabular"/>
-            <output name="METRICS_FILE_NAME" file="summary_SE.txt" ftype="tabular" lines_diff="4">
+            <output name="METRICS_FILE_NAME" file="summary_SE.txt" ftype="tabular" lines_diff="4"/>
+            <output name="DEMULTIPLEX_RESULTS" ftype="tabular">
                 <discovered_dataset designation="unassigned_1" file="unassigned_1_SE.txt" />
             </output>
         </test>
@@ -75,11 +76,11 @@
             <param name="BRED" value="false"/>
 
             <param name="COLLECT_OUTPUTS" value="false" />
-
             <param name="barcode_list_type_con" value="text"/>
             <param name="barcode_text"
                 value="sample1 CACTGT:GTATAG&#10;sample2 ATTCCG:TCCGTC&#10;sample3 GCTACC:TGGTCA&#10;sample4 CGAAAC:CACTGT"/>
-            <output name="METRICS_FILE_NAME" file="summary_PE.txt" ftype="tabular" lines_diff="4">
+            <output name="METRICS_FILE_NAME" file="summary_PE.txt" ftype="tabular" lines_diff="4"/>
+            <output name="DEMULTIPLEX_RESULTS" ftype="tabular">
                 <discovered_dataset designation="unassigned_1" file="unassigned_1_PE.txt" />
                 <discovered_dataset designation="unassigned_2" file="unassigned_2_PE.txt" />
                 <discovered_dataset designation="sample4_CGAAACCACTGT_2" file="sample4_CGAAACCACTGT_2.txt"/>
@@ -101,7 +102,6 @@
             <param name="BPOS" value="BOTH"/>
             <param name="BM" value="BOTH"/>
             <param name="BRED" value="false"/>
-
             <param name="barcode_list_type_con" value="text"/>
             <param name="barcode_text"
                    value="sample1 CACTGT:GTATAG&#10;sample2 ATTCCG:TCCGTC&#10;sample3 GCTACC:TGGTCA&#10;sample4 CGAAAC:CACTGT"/>
@@ -133,6 +133,7 @@ Input files are fastq files, and can be in gzip compressed format.
 Author: Charles Girardot  (charles.girardot@embl.de).
 
 Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
+With contributions by: Mehmet Tekman (@mtekman)
 
 ------
 

src/galaxy/macros.xml

 <macros>
 
-    <token name="@VERSION_STRING@">1.2</token>
+    <token name="@VERSION_STRING@">1.2.1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="1.2">je-suite</requirement>
@@ -278,21 +278,19 @@ ${from_text_area}</configfile>
     </xml>
 
     <token name="@demultiplexer_common_output_options_cmd@">
-        KEEP_UNASSIGNED_READ=$KEEP_UNASSIGNED_READ
-        STATS_ONLY=${adv_options.STATS_ONLY}
-        #if str( $adv_options.DIAG ) == "true":
+        KEEP_UNASSIGNED_READ=${KEEP_UNASSIGNED_READ}
+        STATS_ONLY=${STATS_ONLY}
+        #if str( $DIAG ) == "true":
             BARCODE_DIAG_FILE=$BARCODE_DIAG_FILE
         #end if
     </token>
     <xml name="demultiplexer_common_output_options">
+        <!--<section name="output_options" title="Output Options" expanded="True">-->
+            <param name="COLLECT_OUTPUTS" type="boolean"
+                   truevalue="true" falsevalue="false" checked="false"
+                   label="Output forward and reverse reads in dataset collections" />
             <param name="KEEP_UNASSIGNED_READ" type="boolean" label="Keep unassigned reads (KEEP_UNASSIGNED_READ)"
-            truevalue="true"
-            falsevalue="false"
-            checked="true"
-        />
-        <param name="COLLECT_OUTPUTS" type="boolean" label="Group forward and reverse reads into seperate collection outputs?" />
-
-        <section name="adv_options" title="Advanced Options" expanded="False">
+                   truevalue="true" falsevalue="false" checked="true"/>
             <param name="DIAG" type="boolean" label="Output barcode match reporting file (DIAG)"
                 truevalue="true" falsevalue="false" checked="false"
                 help="This file will
@@ -302,7 +300,7 @@ ${from_text_area}</configfile>
             <param name="STATS_ONLY" type="boolean" label="Only produce metric and diagnostic reports (STATS_ONLY)"
                 truevalue="true" falsevalue="false" checked="false"
                 help="do not demultiplex." />
-        </section>
+        <!--</section>-->
     </xml>
 
     <token name="@common_options_cmd@">
@@ -337,20 +335,20 @@ ${from_text_area}</configfile>
     </token>
 
     <xml name="demultiplexer_common_outputs">
-        <data name="METRICS_FILE_NAME" format="tabular" label="Je-Demultiplex result">
-            <filter>COLLECT_OUTPUTS == False</filter>
-            <!--<discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" ext="fastqsanger"-->
+        <data name="DEMULTIPLEX_RESULTS" format="tabular" label="Je-Demultiplex result placeholder" hidden="true">
+            <filter>COLLECT_OUTPUTS == False and STATS_ONLY == False</filter>
             <discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" directory="results" visible="true" ext="fastqsanger"/>
         </data>
+        <data name="METRICS_FILE_NAME" format="tabular" label="Je-Demultiplex Metrics"/>
         <data name="BARCODE_DIAG_FILE" format="tabular" label="Barcode statistics">
-            <filter>(adv_options['DIAG'] == 'true')</filter>
+            <filter>DIAG</filter>
         </data>
         <collection name="COLLECTION_1" type="list" label="${tool.name} on ${on_string} : Reads_1" >
-            <filter>COLLECT_OUTPUTS</filter>
+            <filter>COLLECT_OUTPUTS and STATS_ONLY == False</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.+_1\..+)" ext="fastqsangar" directory="results" visible="false" />
         </collection>
         <collection name="COLLECTION_2" type="list" label="${tool.name} on ${on_string} : Reads_2" >
-            <filter>COLLECT_OUTPUTS</filter>
+            <filter>COLLECT_OUTPUTS and STATS_ONLY == False</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.+_2\..+)" ext="fastqsangar" directory="results" visible="false" />
         </collection>
     </xml>