diff NmrBucketing_xml.xml @ 4:d61f6ceef5d6 draft

planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty

--- a/NmrBucketing_xml.xml	Fri Aug 12 05:47:27 2016 -0400
+++ b/NmrBucketing_xml.xml	Tue Nov 22 05:22:03 2016 -0500
@@ -1,9 +1,8 @@
-<tool id="NmrBucketing" name="NMR_Bucketing" version="1.0.2">
+<tool id="NmrBucketing" name="NMR_Bucketing" version="1.0.3">
 
     <description> Bucketing and integration of NMR Bruker raw data</description>
 
     <requirements>
-        <requirement type="package" version="3.1.2">R</requirement>
 	    <requirement type="package" version="1.1_4">r-batch</requirement>
 	    <requirement type="package" version="1.8.8">r-pracma</requirement>
     </requirements>
@@ -13,12 +12,14 @@
     </stdio>
 
     <command>
-        Rscript $__tool_directory__/NmrBucketing_wrapper.R
+        Rscript '$__tool_directory__/NmrBucketing_wrapper.R'
 
         #if $inputs.input == "lib":
-            library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library
+            library '$__app__.config.user_library_import_dir/$__user_email__/$inputs.library'
+        #elif $inputs.input == "tsv_file":
+            tsvfile '$inputs.tsv_file'
         #elif $inputs.input == "zip_file":
-            zipfile $inputs.zip_file
+            zipfile '$inputs.zip_file'
         #end if
 
 
@@ -44,21 +45,25 @@
 
         ## Outputs
         logOut log.log
-        dataMatrixOut $dataMatrixOut
-        sampleOut $sampleOut
-        variableOut $variableOut
-        graphOut $graphOut; cat log.log
+        dataMatrixOut '$dataMatrixOut'
+        sampleOut '$sampleOut'
+        variableOut '$variableOut'
+        graphOut '$graphOut'; cat log.log
     </command>
 
     <inputs>
         <conditional name="inputs">
             <param name="input" type="select" label="Choose your inputs method" >
                 <option value="zip_file" selected="true">Zip file from your history containing your Bruker directories</option>
+                <option value="tsv_file">Tsv file containing preprocessed spectra (from your history)</option>
                 <option value="lib" >Library directory name</option>
             </param>
             <when value="zip_file">
                 <param name="zip_file" type="data" format="no_unzip.zip" label="Zip file" />
             </when>
+            <when value="tsv_file">
+                <param name="tsv_file" type="data" format="tabular" label="Tsv file" />
+            </when>
             <when value="lib">
                 <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" >
                     <validator type="empty_field"/> 
@@ -103,7 +108,6 @@
             <filter> graphType != "None" </filter>
         </data>
     </outputs>
-
     
     <tests>
         <test>
@@ -147,12 +151,11 @@
 
 **Upstream tools**
 
-========================= ================= ======= =========
-Name                      output file       format  parameter
-========================= ================= ======= =========
-NA                        NA                zip      NA				
-========================= ================= ======= =========
-
+========================= ============================ =======
+Name                      output file                  format 
+========================= ============================ =======
+NMRAlignment              NMR_Alignment_alignedSpectra tsv    
+========================= ============================ =======
 
 **Downstream tools**
 
@@ -178,13 +181,16 @@
 +===========================+============+
 | 1 : Choose your inputs    |   zip      |
 +---------------------------+------------+
+| 1 : Choose your inputs    |   tsv      |
++---------------------------+------------+
 
 **Choose your inputs**
 
-You have two methods for your inputs:
+You have three methods for your inputs:
 
-| Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
+| Zip file (recommended): You can put a zip file containing your inputs as raw Bruker files: myinputs.zip (containing all your conditions as sub-directories).
 | library folder: You must specify the name of your "library" (folder) created within your space project (for example: /projet/externe/institut/login/galaxylibrary/yourlibrary). Your library must contain all your conditions as sub-directories.
+| Tsv file: You can put a tsv file containing your inputs as preprocessed spectra: myinputs.tsv (containing all your conditions in columns and chemical shifts in rows).
 
 .. image:: ./static/images/Mth_Architecture_Repertoire_Bruker.png
 :width: 800
@@ -275,6 +281,10 @@
 Changelog/News
 --------------
 
+**Version 1.0.3 - 24/10/2016**
+
+- ENHANCEMENT: add possibility of bucketing processed files (upstream tools)	    
+	    
 **Version 1.0.2 - 12/08/2016**
 
 - ENHANCEMENT: x-axis customization: add chemical shift labels