Mercurial > repos > lecorguille > xcms_group

diff abims_xcms_group.xml @ 32:68282292acc4 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
author lecorguille
date Tue, 03 Apr 2018 11:39:07 -0400
parents f248fd3b89d6
children aeba79c716b1
line wrap: on
line diff
--- a/abims_xcms_group.xml	Thu Mar 08 05:53:40 2018 -0500
+++ b/abims_xcms_group.xml	Tue Apr 03 11:39:07 2018 -0400
@@ -4,13 +4,14 @@
 
     <macros>
         <import>macros.xml</import>
+        <import>macros_xcms.xml</import>
     </macros>
 
     <expand macro="requirements"/>
     <expand macro="stdio"/>
 
     <command><![CDATA[
-        @COMMAND_XCMS_SCRIPT@/xcms_group.r
+        @COMMAND_RSCRIPT@/xcms_group.r
         image '$image'
 
         method $methods.method
@@ -41,7 +42,7 @@
    ]]></command>
 
     <inputs>
-        <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks or adjustRtime" />
+        <param name="image" type="data" format="rdata.xcms.findchrompeaks,rdata.xcms.group,rdata.xcms.retcor,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks or adjustRtime" />
         <conditional name="methods">
             <param name="method" type="select" label="Method to use for grouping" help="See the help section below">
                 <option value="PeakDensity" selected="true">PeakDensity - peak grouping based on time dimension peak densities</option>
@@ -84,9 +85,9 @@
     </outputs>
 
     <tests>
-        <!-- from xcmsSet -->
+        <!-- from xcmsSet
         <test>
-            <param name="image" value="faahKO-single-class.xset.merged.RData"/>
+            <param name="image" value="faahKO-single-class.xset.merged.RData" ftype="rdata"/>
             <conditional name="methods">
                 <param name="method" value="PeakDensity"/>
                 <param name="bw" value="5"/>
@@ -116,10 +117,10 @@
             </assert_stdout>
             <output name="variableMetadata" file="faahKO.xset.group.variableMetadata.tsv" />
             <output name="dataMatrix" file="faahKO.xset.group.dataMatrix.tsv" />
-        </test>
+        </test>-->
         <!-- DISABLE FOR TRAVIS
         <test>
-            <param name="image" value="faahKO-single.xset.merged.RData"/>
+            <param name="image" value="faahKO-single.xset.merged.RData" ftype="rdata"/>
             <conditional name="methods">
                 <param name="method" value="PeakDensity"/>
                 <param name="bw" value="5"/>
@@ -143,7 +144,7 @@
         -->
         <!-- DISABLE FOR TRAVIS Zip from xcmsSet
         <test>
-            <param name="image" value="faahKO.xset.RData"/>
+            <param name="image" value="faahKO.xset.RData" ftype="rdata"/>
             <conditional name="methods">
                 <param name="method" value="PeakDensity"/>
                 <param name="bw" value="5"/>
@@ -176,7 +177,7 @@
 
         <!-- DISABLE FOR TRAVIS Zip from retcor
         <test>
-            <param name="image" value="faahKO.xset.group.retcor.RData"/>
+            <param name="image" value="faahKO.xset.group.retcor.RData" ftype="rdata"/>
             <conditional name="methods">
                 <param name="method" value="PeakDensity"/>
                 <param name="bw" value="5"/>
@@ -200,7 +201,7 @@
         -->
         <!-- from retcor -->
         <test>
-            <param name="image" value="faahKO-single.xset.merged.group.retcor.RData"/>
+            <param name="image" value="faahKO-single.xset.merged.group.retcor.RData" ftype="rdata"/>
             <conditional name="methods">
                 <param name="method" value="PeakDensity"/>
                 <param name="bw" value="5"/>
@@ -227,7 +228,7 @@
         <!-- DISABLE FOR TRAVIS
         Test to test the different methods parameters
         <test expect_failure="True">
-            <param name="image" value="faahKO-single.xset.merged.group.retcor.RData"/>
+            <param name="image" value="faahKO-single.xset.merged.group.retcor.RData" ftype="rdata"/>
             <conditional name="methods">
                 <param name="method" value="MzClust"/>
                 <param name="ppm" value="21"/>
@@ -240,7 +241,7 @@
             </assert_stdout>
         </test>
         <test>
-            <param name="image" value="faahKO-single.xset.merged.group.retcor.RData"/>
+            <param name="image" value="faahKO-single.xset.merged.group.retcor.RData" ftype="rdata"/>
             <conditional name="methods">
                 <param name="method" value="NearestPeaks"/>
                 <param name="mzVsRtBalance" value="11"/>
@@ -275,46 +276,32 @@
 
 **Upstream tools**
 
-========================= ================= =================== ==========
-Name                      output file       format              parameter
-========================= ================= =================== ==========
-xcms.xcmsSet              xset.RData        rdata.xcms.raw      RData file
-------------------------- ----------------- ------------------- ----------
-xcms.xcmsSet Merger       xset.RData        rdata.xcms.raw      RData file
-------------------------- ----------------- ------------------- ----------
-xcms.retcor               xset.RData        rdata.xcms.retcor   RData file
-========================= ================= =================== ==========
+========================= ================= ============================== ==========
+Name                      output file       format                         parameter
+========================= ================= ============================== ==========
+xcms.xcmsSet              xset.RData        rdata.xcms.findchrompeaks      RData file
+------------------------- ----------------- ------------------------------ ----------
+xcms.xcmsSet Merger       xset.RData        rdata.xcms.findchrompeaks      RData file
+------------------------- ----------------- ------------------------------ ----------
+xcms.retcor               xset.RData        rdata.xcms.retcor              RData file
+========================= ================= ============================== ==========
 
 
 **Downstream tools**
 
-+---------------------------+--------------------------------------+
-| Name                      | Output file     | Format             |
-+===========================+=================+====================+
-|xcms.retcor                | xset.RData      | rdata.xcms.group   |
-+---------------------------+--------------------------------------+
-|xcms.fillPeaks             | xset.RData      | rdata.xcms.group   |
-+---------------------------+--------------------------------------+
-
-The output file is an xcmsSet.RData file. You can continue your analysis using it in **xcms.retcor** tool as an next step and then **xcms.fillPeaks**.
+=========================== ================= ====================
+Name                        Output file       Format
+=========================== ================= ====================
+xcms.retcor                 xset.RData        rdata.xcms.group
+--------------------------- ----------------- --------------------
+xcms.fillPeaks              xset.RData        rdata.xcms.group
+=========================== ================= ====================
 
 **General schema of the metabolomic workflow**
 
 .. image:: xcms_group_workflow.png
 
-
------------
-Input files
------------
-
-+---------------------------+-----------------------+
-| Parameter : num + label   |   Format              |
-+===========================+=======================+
-| Or : RData file            |   rdata.xcms.raw     |
-+---------------------------+-----------------------+
-| Or : RData file            |   rdata.xcms.retcor  |
-+---------------------------+-----------------------+
-
+---------------------------------------------------
 
 ----------
 Parameters
@@ -350,52 +337,15 @@
 Output files
 ------------
 
-xset.group.Rplots.pdf
-
 xset.group.RData: rdata.xcms.group format
 
     | Rdata file that will be necessary in the third and fourth step of the workflow (xcms.retcor and xcms.fillpeaks).
 
-
-------
-
-.. class:: infomark
-
-The output file is an xset.group.RData file. You can continue your analysis using it in **xcms.retcor** tool.
-
-
----------------------------------------------------
-
-
----------------
-Working example
----------------
-
-Input files
------------
-
-    | RData file -> **xset.RData**
+xset.group.plotChromPeakDensity.pdf
 
-Parameters
-----------
-
-    | Method -> **density**
-    | bw     -> **5**
-    | minFraction -> **0.3**
-    | binSize    -> **0.01**
-    | Advanced options: **show**
-    | maxFeatures -> **50**
+    | Density plot
 
-
-Output files
-------------
-
-    | **1) xset.RData: RData file**
-
-    | **2) Example of an xset.group.Rplots pdf file**
-
-.. image:: xcms_group.png
-        :width: 700
+@HELP_PEAKLIST_OUTPUT@
 
 
 ---------------------------------------------------