diff abims_xcms_xcmsSet.xml @ 1:2f5b78be1dd6 draft

Uploaded

--- a/abims_xcms_xcmsSet.xml	Fri Aug 07 07:48:57 2015 -0400
+++ b/abims_xcms_xcmsSet.xml	Wed Dec 23 11:04:37 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.2">
+<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.5">
     
     <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>
     
@@ -13,7 +13,7 @@
         <exit_code range="1:" level="fatal" />
     </stdio>
     
-    <command>
+    <command><![CDATA[
         xcms.r
         #if $inputs.input == "lib":
             library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library
@@ -22,6 +22,12 @@
         #end if
 
         xfunction xcmsSet
+
+        xsetRdataOutput $xsetRData
+        sampleMetadataOutput $sampleMetadata
+        ticspdf $ticsRawPdf
+        bicspdf $bpcsRawPdf
+
         ## profmethod $profmethod 
         nSlaves \${GALAXY_SLOTS:-1} method $methods.method 
         #if $methods.method == "centWave":
@@ -29,14 +35,14 @@
             peakwidth "c($methods.peakwidth)"
         #if $methods.options_scanrange.option == "show":
                 scanrange "c($methods.options_scanrange.scanrange)"
-            #end if 
-            #if $methods.options_c.option == "show":
-                mzdiff $methods.options_c.mzdiff
-                snthresh $methods.options_c.snthresh
-                integrate $methods.options_c.integrate
-                noise $methods.options_c.noise
-                prefilter "c($methods.options_c.prefilter)"
-            #end if
+        #end if 
+        #if $methods.options_c.option == "show":
+            mzdiff $methods.options_c.mzdiff
+            snthresh $methods.options_c.snthresh
+            integrate $methods.options_c.integrate
+            noise $methods.options_c.noise
+            prefilter "c($methods.options_c.prefilter)"
+        #end if
         #elif $methods.method == "matchedFilter":
             step $methods.step
             fwhm $methods.fwhm
@@ -56,13 +62,12 @@
             scales "c($methods.scales)"
             SNR.method "$methods.SNR_method"
         #end if
-        &amp;&amp; (mv xcmsSet.RData $xsetRData;
-        mv sampleMetadata.tsv $sampleMetadata;
-        mv TICs_raw.pdf $ticsRawPdf;
-        mv BPCs_raw.pdf $bpcsRawPdf;
-        mv xset.log $log);
-        cat $log
-    </command>
+        ;
+        return=\$?;
+        mv log.txt $log;
+        cat $log;
+        sh -c "exit \$return"
+    ]]></command>
     
     <inputs>
 
@@ -113,6 +118,8 @@
                             <validator type="empty_field"/> 
                         </param>
                     </when>
+                    <when value="hide">
+                    </when>
                 </conditional>
                         
                 <conditional name="options_c">
@@ -130,6 +137,8 @@
                         <param name="prefilter" type="text" value="3,100" label="Prefilter step for the first phase" help="[prefilter] Separate by coma k,I. Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’"/>
                         <param name="noise" type="integer" value="0" label="Noise filter" help="[noise] optional argument which is useful for data that was centroided without any intensity threshold, centroids with intensity smaller than ‘noise’ are omitted from ROI detection"/>
                     </when>
+                    <when value="hide">
+                    </when>
                 </conditional>
             </when>
 
@@ -153,6 +162,8 @@
                         <param name="mzdiff" type="text" size="20" value="0.8-step*steps" label="m/z difference" help="min m/z difference for peaks with overlapping RT " />
 -->
                     </when>
+                    <when value="hide">
+                    </when>
                 </conditional>
             </when>
 
@@ -190,15 +201,24 @@
             <param name="methods.options_m.max" value="50" />
             <param name="methods.options_m.snthresh" value="1" />
             <param name="methods.options_m.steps" value="2" />
-            <output name="xsetRData" file="xset.RData" />
-            <output name="sampleMetadata" file="sampleMetadata.tsv" />
-            <output name="ticsRawPdf" file="xset.TICs_raw.pdf" />
-            <output name="bpcsRawPdf" file="xset.BPCs_raw.pdf" />
-            <output name="log" file="xset.log.txt" />
+            <!--<output name="xsetRData" file="xset.RData" />-->
+            <!--<output name="sampleMetadata" file="sampleMetadata.tsv" />-->
+            <!--<output name="ticsRawPdf" file="xset.TICs_raw.pdf" />-->
+            <!--<output name="bpcsRawPdf" file="xset.BPCs_raw.pdf" />-->
+            <output name="log">
+                <assert_contents>
+                    <has_text text="object with 9 samples" />
+                    <has_text text="Time range: 0.7-1140 seconds (0-19 minutes)" />
+                    <has_text text="Mass range: 50.0019-999.9863 m/z" />
+                    <has_text text="Peaks: 135846 (about 15094 per sample)" />
+                    <has_text text="Peak Groups: 0" />
+                    <has_text text="Sample classes: bio, blank" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
     
-    <help>
+    <help><![CDATA[
 
 .. class:: infomark
 
@@ -392,7 +412,7 @@
 .. image:: xcms_tics.png
 
 
-    </help>
+    ]]></help>
 
 
     <citations>