--- a/damidseq_core.xml	Wed Apr 18 15:02:42 2018 -0400
+++ b/damidseq_core.xml	Fri Apr 20 06:14:00 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="damidseq_core" name="damidseq" version="0.1.3">
+<tool id="damidseq_core" name="damidseq" version="0.1.4">
     <description>align, extend and normalize a DamID-seq experiment</description>
     <requirements>
         <requirement type="package" version="1.4">damidseq_pipeline</requirement>
@@ -30,7 +30,10 @@
         --qscore1min=$qscore1min
         --qscore2max=$qscore2max
         --threads=\${GALAXY_SLOTS:-4} 2>&1| LC_ALL=C sed -e 's/[^A-Za-z0-9._-]/ /g' &&
-        mv Fusion-vs-Dam.* fusion.output
+        mv Fusion-vs-Dam.gatc.* gatc.output
+        #if str($full_data_files):
+            && mv Fusion-vs-Dam.* full.output
+        #end if
     ]]></command>
     <configfiles>
         <configfile name="index">A1	Dam
@@ -55,7 +58,7 @@
             <option value="gatc">To nearest GATC site</option>
             <option value="full">Full</option>
         </param>
-        <param argument="--full_data_files" type="boolean" truevalue="--full_data_file" falsevalue="" label="Output full binned ratio files (not only GATC array)"/>
+        <param argument="--full_data_files" type="boolean" truevalue="--full_data_files" falsevalue="" label="Output full binned ratio files (not only GATC array)"/>
         <param argument="--len" type="integer" min="50" value="300" label="Length to extend reads to"/>
         <param argument="--bins" type="integer" min="10" value="75" label="Width of bins to use for mapping reads"/>
         <param argument="--min_norm_value" type="float" value="-5.0" label="Minimum log2 value to limit normalisation search at"/>
@@ -72,7 +75,7 @@
         <param argument="--qscore2max" type="float" min="0.0" value="0.9" max="1.0" label="max decile for normalising from fusion-protein array"/>
     </inputs>
     <outputs>
-        <data name="output_ratio" format="bed" from_work_dir="fusion.output" label="Dam-fusion vs Dam-only ratio">
+        <data name="output_ratio" format="bedgraph" from_work_dir="gatc.output" label="Dam-fusion vs Dam-only GATC ratio on ${on_string}">
             <change_format>
                 <when input="output_format" value="gff" format="gff" />
             </change_format>
@@ -85,7 +88,11 @@
                 </action>
             </actions>
         </data>
-        <data name="control_output" format="bam" from_work_dir="Dam-ext300.bam" label="Dam-only alignment">
+        <data name="output_ratio_full" format="bedgraph" from_work_dir="full.output" label="Dam-fusion vs Dam-only full ratio on ${on_string}">
+            <filter>full_data_files == '--full_data_files'</filter>
+            <change_format>
+                <when input="output_format" value="gff" format="gff" />
+            </change_format>
             <actions>
                 <action type="metadata" name="dbkey">
                     <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
@@ -95,7 +102,17 @@
                 </action>
             </actions>
         </data>
-        <data name="fusion_output" format="bam" from_work_dir="Fusion-ext300.bam" label="Dam-fusion alignment">
+        <data name="control_output" format="bam" from_work_dir="Dam-ext300.bam" label="Dam-only alignment on ${on_string}">
+            <actions>
+                <action type="metadata" name="dbkey">
+                    <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
+                        <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                        <filter type="param_value" ref="reference_index" column="0"/>
+                    </option>
+                </action>
+            </actions>
+        </data>
+        <data name="fusion_output" format="bam" from_work_dir="Fusion-ext300.bam" label="Dam-fusion alignment on ${on_string}">
             <actions>
                 <action type="metadata" name="dbkey">
                     <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
@@ -123,7 +140,9 @@
             <param name="gatc_frag_file" value="dm6.GATC.gff"/>
             <param name="reference_index" value="dm6"/>
             <param name="norm_method" value="rpm"/>
+            <param name="full_data_files" value="true"/>
             <output name="output_ratio" file="output_ratio.bed"/>
+            <output name="output_ratio_full" file="output_ratio_full.bed"/>
             <output name="control_output" file="control.bam"/>
             <output name="fusion_output" file="fusion.bam"/>
         </test>