diff abims_CAMERA_annotateDiffreport.xml @ 1:a887bff50e45 draft

Uploaded

--- a/abims_CAMERA_annotateDiffreport.xml	Fri Aug 07 09:08:29 2015 -0400
+++ b/abims_CAMERA_annotateDiffreport.xml	Tue Jan 19 08:32:29 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.0.1">
+<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.2">
 
     <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description>
     
@@ -14,10 +14,17 @@
         <exit_code range="1:" level="fatal" />
     </stdio>
 
-    <command>
+    <command><![CDATA[
         CAMERA.r 
-        xfunction annotatediff image $image
-        convert_param $convert_param num_digits $num_digits nSlaves \${GALAXY_SLOTS:-1}
+        xfunction annotatediff 
+        image $image
+
+        variableMetadataOutput $variableMetadata
+        dataMatrixOutput $datamatrix
+        xsetRdataOutput $rdata
+
+        convert_param $convert_param num_digits $num_digits 
+        nSlaves \${GALAXY_SLOTS:-1}
         sigma $sigma perfwhm $perfwhm 
         maxcharge $maxcharge maxiso $maxiso minfrac $minfrac
         ppm $ppm mzabs $mzabs intval $intval 
@@ -42,6 +49,7 @@
             h $options.h
             w $options.w
             mzdec $options.mzdec
+            new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_
         #else
             eicmax 0
             eicwidth 200
@@ -50,16 +58,11 @@
             h 480
             w 640
             mzdec 2
+            new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_
         #end if
-        &amp;&amp; (
-            mv variableMetadata.tsv $variableMetadata;
-            mv dataMatrix.tsv $datamatrix;
-            mv annotatediff.RData $rdata
-        );
-        cat xset.log
         
       
-    </command>
+    ]]></command>
 
     <inputs>
     
@@ -67,7 +70,7 @@
         <param name="image" type="data" label="RData file" format="rdata.xcms.fillpeaks,rdata" help="output file from another function xcms (fillPeaks)" />
 
         <param name="convert_param" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
-        <param name="num_digits" type="integer" value="0" label="" help="Number of decimal places for mass values reported in ions identifiers" />
+        <param name="num_digits" type="integer" value="4" label="" help="Number of decimal places for mass values reported in ions identifiers. A minimum of 4 decimal places should be set" />
 
         <param name="sigma" type="integer" value="6" label="groupFWHM: multiplier of the standard deviation" help="[sigma]" />
         <param name="perfwhm" type="float" value="0.6" max="1" min="0" label="groupFWHM: percentage of FWHM width" help="[perfwhm]" />
@@ -137,16 +140,17 @@
     </inputs>
 
     <outputs>
-        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" >
-            <discover_datasets pattern="__designation_and_ext__" directory="zip" visible="true" />
-        </data>
+        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" />
         <data name="datamatrix" format="tabular" label="${image.name[:-6]}.annotate.dataMatrix.tsv" />
         <data name="rdata" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.polarity}.Rdata" >
             <change_format>
                 <when input="quick_block.polarity" value="positive" format="rdata.camera.positive" />
                 <when input="quick_block.polarity" value="negative" format="rdata.camera.negative" />
             </change_format>
-        </data>    
+        </data>
+	<data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="True">
+		 <filter>(options['option'] == 'show')</filter>
+	</data>    
     </outputs>
     
     <tests>
@@ -188,7 +192,7 @@
     
     
     
-    <help>
+    <help><![CDATA[
         
 .. class:: infomark
 
@@ -373,7 +377,7 @@
 
 .. image:: annotatediffreport_variableMetadata.png
 
-    </help>
+    ]]></help>
 
     <citations>
         <citation type="doi">10.1021/ac202450g</citation>