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changeset 0:022df2ef15b0 draft

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planemo upload
author lecorguille
date Fri, 07 Aug 2015 10:58:46 -0400
parents
children 9e6526027b97
files Makefile abims_xcms_fillPeaks.xml planemo.sh repository_dependencies.xml static/images/xcms_fillpeaks_workflow.png test-data/xset.group.retcor.group.RData test-data/xset.group.retcor.group.fillPeaks.RData tool_dependencies.xml
diffstat 8 files changed, 224 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Makefile	Fri Aug 07 10:58:46 2015 -0400
@@ -0,0 +1,23 @@
+# USAGE: make [install|clean]
+
+# -------- VARIABLE --------
+
+OBJ=xcms_fillpeaks.tgz
+DEP=abims_xcms_fillPeaks.xml tool_dependencies.xml repository_dependencies.xml static test-data
+
+
+# ------------------------
+
+all: $(OBJ)
+
+$(OBJ): $(DEP)
+	tar --exclude=".svn" -zchf $@ $^
+
+# ------------------------
+
+install: $(OBJ)
+	mv *.tgz ~
+
+clean:
+	rm *.tgz
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abims_xcms_fillPeaks.xml	Fri Aug 07 10:58:46 2015 -0400
@@ -0,0 +1,183 @@
+<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.2">
+
+    <description>Integrate the signal in the region of that peak group not represented and create a new peak</description>
+
+    <requirements>
+        <requirement type="package" version="3.1.2">R</requirement>
+        <requirement type="binary">Rscript</requirement>
+        <requirement type="package" version="1.44.0">xcms</requirement>
+        <requirement type="package" version="2.1">xcms_w4m_script</requirement>
+    </requirements>
+    
+    <stdio>
+        <exit_code range="1:" level="fatal" />
+    </stdio>
+
+    <command>
+        xcms.r xfunction fillPeaks image $image method $method &amp;&amp; mv fillPeaks.RData $xsetRData; cat xset.log
+    </command>
+
+    <inputs>
+        <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (group)" />
+        <param name="method" type="select" label="Filling method" help="[method] See the help section below">
+            <option value="chrom" selected="true">chrom</option>
+            <option value="MSW" >MSW</option>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" />
+    </outputs>
+    
+    <tests>
+        <test>
+            <param name="image" value="xset.group.retcor.group.RData"/>
+            <param name="method" value="chrom"/>
+            <output name="xsetRData" file="xset.group.retcor.group.fillPeaks.RData" />
+        </test>
+    </tests>
+
+    <help>
+
+        
+.. class:: infomark
+
+**Authors**  Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu 
+
+.. class:: infomark
+
+**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@univ-nantes.fr - part of Workflow4Metabolomics.org [W4M]
+
+ | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
+
+
+---------------------------------------------------
+
+==============
+Xcms.fillPeaks
+==============
+
+-----------
+Description
+-----------
+
+For each sample, identify peak groups where that sample is not
+represented. For each of those peak groups, integrate the signal
+in the region of that peak group and create a new peak.
+
+According to the type of raw-data there are 2
+different methods available. for filling gcms/lcms data the method
+"chrom" integrates raw-data in the chromatographic domain, whereas
+"MSW" is used for peaklists without retention-time information
+like those from direct-infusion spectra.
+
+
+
+-----------------
+Workflow position
+-----------------
+
+
+**Upstream tools**
+
+========================= ================= ================== ==========
+Name                      output file       format             parameter
+========================= ================= ================== ==========
+xcms.group                xset.group.RData  rdata.xcms.group   RData file
+========================= ================= ================== ==========
+
+
+**Downstream tools**
+
++---------------------------+------------------+-----------------------+
+| Name                      | Output file      | Format                |
++===========================+==================+=======================+
+|xcms.diffreport            | xset.retcor.RData| rdata.xcms.fillpeaks  |
++---------------------------+------------------+-----------------------+
+|xcms.annotateDiffreport    | xset.retcor.RData| rdata.xcms.fillpeaks  |
++---------------------------+------------------+-----------------------+
+
+The output file **xset.fillpeaks** is an RData file. You can continue your analysis using it in **xcms.diffreport** or **xcms.annotateDiffreport** tool as an next step of the workflow.
+
+
+**General schema of the metabolomic workflow**
+
+.. image:: xcms_fillpeaks_workflow.png
+
+
+
+-----------
+Input files
+-----------
+
++---------------------------+-----------------------+
+| Parameter : num + label   |   Format              |
++===========================+=======================+
+| 1 : RData file            |   rdata.xcms.group    |
++---------------------------+-----------------------+
+
+
+----------
+Parameters
+----------
+
+
+Method
+------
+
+**chrom**
+
+    | This method produces intensity values for those missing samples by integrating raw data in peak group region. In a given group, the start and ending retention time points for integration are defined by the median start and end points of the other detected peaks. The start and end m/z values are similarly determined. Intensities can be still be zero, which is a rather unusual intensity for a peak.  This is the case if e.g. the raw data was threshholded, and the integration area contains no actual raw intensities, or if one sample is miscalibrated, such the raw data points are (just) outside the integration area.
+    | Importantly, if retention time correction data is available, the alignment information is used to more precisely integrate the propper region of the raw data. If the corrected retention time is beyond the end of the raw data, the value will be not-a-number (NaN).
+
+**MSW**
+
+    | "MSW" is used for peaklists without retention-time information like those from direct-infusion spectra.
+
+------------
+Output files
+------------
+
+xset.fillPeaks.RData : rdata.xcms.fillpeaks format
+
+    | Rdata file that will be used in the **xcms.diffreport** or **xcms.annotateDiffreport** step of the workflow.
+    
+------
+
+.. class:: infomark 
+
+The output file is an group.RData file. You can continue your analysis using it in **xcms.diffreport** or **xcms.annotateDiffreport** tool.
+
+    
+---------------------------------------------------
+
+---------------
+Working example
+---------------
+
+Input files
+-----------
+
+    | RData file -> **xset.retcor.RData**
+
+Parameters
+----------
+
+    | method -> **chrom**
+    
+
+Output files
+------------
+
+    | **xset.fillPeaks.RData: RData file**
+
+
+    </help>
+
+    <citations>
+        <citation type="doi">10.1021/ac051437y</citation>
+        <citation type="doi">10.1093/bioinformatics/btu813</citation>
+    </citations>
+
+
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/planemo.sh	Fri Aug 07 10:58:46 2015 -0400
@@ -0,0 +1,1 @@
+planemo shed_init -f --name=xcms_fillpeaks --owner=lecorguille --description="[W4M][GC-MS] XCMS R Package - Preprocessing - Integrate areas of missing peaks" --homepage_url="http://workflow4metabolomics.org" --long_description="Part of the W4M project: http://workflow4metabolomics.org\n\nXCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html\n\nFor each sample, identify peak groups where that sample is not represented. For each of those peak groups, integrate the signal in the region of that peak group and create a new peak.\n\nBEWARE: this tool don't come with its script. You will need to install the dedicated package_xcms_w4m_script too" --category="Metabolomics"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Fri Aug 07 10:58:46 2015 -0400
@@ -0,0 +1,5 @@
+<?xml version="1.0"?>
+<repositories>
+    <repository changeset_revision="12afb0ecb55f" name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="d64562a4ebb3" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
+</repositories>
Binary file static/images/xcms_fillpeaks_workflow.png has changed
Binary file test-data/xset.group.retcor.group.RData has changed
Binary file test-data/xset.group.retcor.group.fillPeaks.RData has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Aug 07 10:58:46 2015 -0400
@@ -0,0 +1,12 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="3.1.2">
+        <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="xcms" version="1.44.0">
+        <repository changeset_revision="a1c3fc774157" name="package_r_xcms_1_44_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="xcms_w4m_script" version="2.1">
+        <repository changeset_revision="c94c8ef520c8" name="package_xcms_w4m_script_2_1" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>