--- a/abims_CAMERA_annotateDiffreport.xml	Tue Oct 09 06:03:01 2018 -0400
+++ b/abims_CAMERA_annotateDiffreport.xml	Thu Aug 29 11:38:21 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.4">
+<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.5">
 
     <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description>
 
@@ -10,15 +10,11 @@
     <expand macro="stdio"/>
 
     <command><![CDATA[
-        @COMMAND_CAMERA_SCRIPT@
-        xfunction annotatediff
+        @COMMAND_RSCRIPT@/CAMERA_annotateDiffreport.r
         image '$image'
 
         nSlaves \${GALAXY_SLOTS:-1}
 
-        ## output
-        variableMetadataOutput '$variableMetadata'
-
         ## groupFWHM
         sigma $groupfwhm.sigma
         perfwhm $groupfwhm.perfwhm
@@ -34,8 +30,6 @@
 
         quick $quick_block.quick
         #if $quick_block.quick == "FALSE":
-            xsetRdataOutput '$rdata_quick_false'
-
             ## groupcorr
             cor_eic_th $quick_block.groupcorr.cor_eic_th
             graphMethod $quick_block.groupcorr.graphMethod
@@ -52,8 +46,6 @@
             #else
                 rules $quick_block.findadducts.rules_block.rules
             #end if
-        #else
-            xsetRdataOutput '$rdata_quick_true'
         #end if
 
         #if $diffreport.options.option == "show":
@@ -66,6 +58,8 @@
             h $diffreport.options.h
             w $diffreport.options.w
             mzdec $diffreport.options.mzdec
+            tabular2 $diffreport.options.tabular2
+            png2 $diffreport.options.png2
         #end if
 
         @COMMAND_PEAKLIST@
@@ -159,6 +153,14 @@
                     <param name="w" type="integer" value="640" label="Numeric variable for the width of the eic and boxplots print out made" help="[width]" />
                     <param name="mzdec" type="integer" value="2" label="Number of decimal places of title m/z values in the eic plot" help="[mzdec]" />
                     <param name="sortpval" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="logical indicating whether the reports should be sorted by p-value" help="[sortpval]"/>
+                    <param name="tabular2" type="select" label="Export the Diffreport files in ">
+                        <option value="zip" selected="true">Zip</option>
+                        <option value="datasetcollection">Individual file in a Dataset Collection</option>
+                    </param>
+                    <param name="png2" type="select" label="Export the EIC and boxplots in ">
+                        <option value="zip" selected="true">Zip</option>
+                        <option value="pdf">Individual pdf</option>
+                    </param>
                 </when>
                 <when value="hide">
                 </when>
@@ -170,22 +172,36 @@
     </inputs>
 
     <outputs>
-        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" />
-        <data name="rdata_quick_false" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.findadducts.polarity}.Rdata" >
+        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" />
+        <data name="rdata_quick_false" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.findadducts.polarity}.Rdata"  from_work_dir="annotatediff.RData">
             <filter>quick_block['quick'] == 'FALSE'</filter>
             <change_format>
                 <when input="quick_block.findadducts.polarity" value="positive" format="rdata.camera.positive" />
                 <when input="quick_block.findadducts.polarity" value="negative" format="rdata.camera.negative" />
             </change_format>
         </data>
-        <data name="rdata_quick_true" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.quick.Rdata" >
+        <data name="rdata_quick_true" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.quick.Rdata" from_work_dir="annotatediff.RData">
             <filter>quick_block['quick'] == 'TRUE'</filter>
         </data>
-        <data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="true">
-            <filter>diffreport['options']['option'] == 'show'</filter>
-            <discover_datasets pattern="__designation_and_ext__" directory="pdf" visible="true" />
-            <discover_datasets pattern="__designation_and_ext__" directory="tabular" visible="true" />
+
+        <data name="output_diffreport_eic_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_eic.zip" from_work_dir="eic.zip" >
+            <filter>diffreport['options']['option'] == 'show' and diffreport['options']['png2'] == 'zip'</filter>
+        </data>
+        <data name="output_diffreport_box_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_box.zip" from_work_dir="box.zip" >
+            <filter>diffreport['options']['option'] == 'show' and diffreport['options']['png2'] == 'zip'</filter>
         </data>
+        <collection name="output_diffreport_picture_pdf" type="list" label="${image.name[:-6]}.annotateDiffreport.pdf">
+            <filter>diffreport['options']['option'] == 'show' and diffreport['options']['png2'] == 'pdf'</filter>
+            <discover_datasets pattern="__designation_and_ext__" directory="pdf" format="pdf" />
+        </collection>
+
+        <data name="output_diffreport_table_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_table.zip" from_work_dir="tabular.zip">
+            <filter>diffreport['options']['option'] == 'show' and diffreport['options']['tabular2'] == 'zip'</filter>
+        </data>
+        <collection name="output_diffreport_table_collection" type="list" label="${image.name[:-6]}.annotateDiffreport_table">
+            <filter>diffreport['options']['option'] == 'show' and diffreport['options']['tabular2'] == 'datasetcollection'</filter>
+            <discover_datasets pattern="__designation_and_ext__" directory="tabular" format="tabular" />
+        </collection>
     </outputs>
 
     <tests>
@@ -418,9 +434,19 @@
 Changelog/News
 --------------
 
+.. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS
+
+**Version 2.2.5 - 09/04/2019**
+
+- NEW: zip export are back for pictures (eic and boxplot) and diffreport tables
+
+- UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_)
+
+- UPGRADE: refactoring of internal code
+
 **Version 2.2.4 - 09/10/2018**
 
-- NES: CAMERA.annotate no longer export a DataMatrix. fillChromPeaks does the job
+- NEW: CAMERA.annotate no longer export a DataMatrix. fillChromPeaks does the job
 
 **Version 2.2.3 - 30/04/2018**