diff abims_xcms_xcmsSet.xml @ 17:602acc32b549 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907

--- a/abims_xcms_xcmsSet.xml	Mon Jan 30 08:51:01 2017 -0500
+++ b/abims_xcms_xcmsSet.xml	Sun Feb 05 08:55:49 2017 -0500
@@ -1,5 +1,4 @@
-<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.11">
-
+<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.1.0">
     <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>
 
     <macros>
@@ -11,10 +10,11 @@
 
     <command><![CDATA[
         @COMMAND_XCMS_SCRIPT@
-        #if $inputs.input == "lib":
-            library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library
-        #elif $inputs.input == "zip_file":
+
+        #if $inputs.input == "zip_file":
             zipfile $inputs.zip_file
+        #elif $inputs.input == "single_file":
+            singlefile_galaxyPath $inputs.single_file singlefile_sampleName $inputs.single_file.name
         #end if
 
         xfunction xcmsSet
@@ -65,20 +65,17 @@
 
     <inputs>
 
-        <conditional name="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 chromatograms</option>
-                <option value="lib" >Library directory name</option>
+                <option value="single_file">mzXML file from your history</option>
             </param>
             <when value="zip_file">
                 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip 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"/>
-            </param>
-                </when>
-
+            </when>
+            <when value="single_file">
+                <param name="single_file" type="data" format="mzxml,netcdf" label="Single file" />
+            </when>
         </conditional>
 
         <conditional name="options_scanrange">
@@ -103,7 +100,6 @@
             <option value="binlinbase">binlinbase</option>
             <option value="intlin">intlin</option>
         </param>
-        <param name="nSlaves" type="integer" value="9" label="MPI-slaves CPU" help="number of MPI-slaves to use for parallel peak detection" />
 -->
         <conditional name="methods">
             <param name="method" type="select" label="Extraction method for peaks detection" help="[method] See the help section below">
@@ -116,7 +112,7 @@
             <when value="centWave">
                 <param name="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="[ppm]" />
                 <param name="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="[peakwidth]" />
-                
+
                 <conditional name="options_c">
                     <param name="option" type="select" label="Advanced options" >
                         <option value="show">show</option>
@@ -241,6 +237,109 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- Passed by disable to save time for Travis"
+        <!--<test>
+            <param name="inputs|input" value="single_file" />
+            <param name="inputs|single_file" value="ko15.CDF"  ftype="netcdf" />
+            <param name="methods|method" value="centWave" />
+            <param name="methods|ppm" value="25" />
+            <param name="methods|peakwidth" value="20,50" />
+            <output name="log">
+                <assert_contents>
+                    <has_text text="object with 1 samples" />
+                    <has_text text="Time range: 2506.1-4471.7 seconds (41.8-74.5 minutes)" />
+                    <has_text text="Mass range: 200.2-600 m/z" />
+                    <has_text text="Peaks: 2262 (about 2262 per sample)" />
+                    <has_text text="Peak Groups: 0" />
+                    <has_text text="Sample classes: ." />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="inputs|input" value="single_file" />
+            <param name="inputs|single_file" value="ko16.CDF"  ftype="netcdf" />
+            <param name="methods|method" value="centWave" />
+            <param name="methods|ppm" value="25" />
+            <param name="methods|peakwidth" value="20,50" />
+            <output name="log">
+                <assert_contents>
+                    <has_text text="object with 1 samples" />
+                    <has_text text="Time range: 2521.7-4477.9 seconds (42-74.6 minutes)" />
+                    <has_text text="Mass range: 200.1-600 m/z" />
+                    <has_text text="Peaks: 2408 (about 2408 per sample)" />
+                    <has_text text="Peak Groups: 0" />
+                    <has_text text="Sample classes: ." />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="inputs|input" value="single_file" />
+            <param name="inputs|single_file" value="wt15.CDF"  ftype="netcdf" />
+            <param name="methods|method" value="centWave" />
+            <param name="methods|ppm" value="25" />
+            <param name="methods|peakwidth" value="20,50" />
+            <output name="log">
+                <assert_contents>
+                    <has_text text="object with 1 samples" />
+                    <has_text text="Time range: 2517-4473.2 seconds (42-74.6 minutes)" />
+                    <has_text text="Mass range: 200.2-599.8 m/z" />
+                    <has_text text="Peaks: 2278 (about 2278 per sample)" />
+                    <has_text text="Peak Groups: 0" />
+                    <has_text text="Sample classes: ." />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="inputs|input" value="single_file" />
+            <param name="inputs|single_file" value="wt16.CDF"  ftype="netcdf" />
+            <param name="methods|method" value="centWave" />
+            <param name="methods|ppm" value="25" />
+            <param name="methods|peakwidth" value="20,50" />
+            <output name="log">
+                <assert_contents>
+                    <has_text text="object with 1 samples" />
+                    <has_text text="Time range: 2521.7-4468.5 seconds (42-74.5 minutes)" />
+                    <has_text text="Mass range: 200.3-600 m/z" />
+                    <has_text text="Peaks: 2303 (about 2303 per sample)" />
+                    <has_text text="Peak Groups: 0" />
+                    <has_text text="Sample classes: ." />
+                </assert_contents>
+            </output>
+        </test>-->
+        <test>
+            <param name="inputs|input" value="single_file" />
+            <param name="inputs|single_file" value="HU_neg_017.mzXML"  ftype="mzxml" />
+            <param name="methods|method" value="centWave" />
+            <param name="methods|ppm" value="25" />
+            <param name="methods|peakwidth" value="20,50" />
+            <output name="log">
+                <assert_contents>
+                    <has_text text="object with 1 samples" />
+                    <has_text text="Time range: 3.5-1139.1 seconds (0.1-19 minutes)" />
+                    <has_text text="Mass range: 57.9756-556.8128 m/z" />
+                    <has_text text="Peaks: 380 (about 380 per sample)" />
+                    <has_text text="Peak Groups: 0" />
+                    <has_text text="Sample classes: ." />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="inputs|input" value="single_file" />
+            <param name="inputs|single_file" value="MM14.mzML"  ftype="mzxml" />
+            <param name="methods|method" value="centWave" />
+            <param name="methods|ppm" value="56" />
+            <param name="methods|peakwidth" value="5.275,13.5" />
+            <output name="log">
+                <assert_contents>
+                    <has_text text="object with 1 samples" />
+                    <has_text text="Time range: 271-307.3 seconds (4.5-5.1 minutes)" />
+                    <has_text text="Mass range: 117.0357-936.7059 m/z" />
+                    <has_text text="Peaks: 222 (about 222 per sample)" />
+                    <has_text text="Peak Groups: 0" />
+                    <has_text text="Sample classes: ." />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
 
     <help><![CDATA[
@@ -306,21 +405,23 @@
 Input files
 -----------
 
-+---------------------------+------------+
-| Parameter : num + label   |   Format   |
-+===========================+============+
-| 1 : Choose your inputs    |   zip      |
-+---------------------------+------------+
++---------------------------+--------------------+
+| Parameter : num + label   |   Format           |
++===========================+====================+
+| OR : Zip file             |   zip              |
++---------------------------+--------------------+
+| OR : Single file          |   mzXML, netCDF    |
++---------------------------+--------------------+
 
 **Choose your inputs**
 
 You have two 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).
-    | 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.
+    | Single file: You can put a single file as input. That way, you will be able to launch several xcmsSet in parallel and use "xcms.xcmsSet Merger" before "xcms.group"
 
-Steps for creating the zip file
--------------------------------
+Zip file: Steps for creating the zip file
+-----------------------------------------
 
 **Step1: Creating your directory and hierarchize the subdirectories**
 
@@ -478,6 +579,10 @@
 Changelog/News
 --------------
 
+**Version 2.1.0 - 03/02/2017**
+
+- NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group".
+
 **Version 2.0.11 - 22/12/2016**
 
 - BUGFIX: propose scanrange for all methods