svn2git

galaxy/camera_annotate/.shed.yml

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+categories: [Metabolomics]
+description: '[W4M][LC-MS] CAMERA R Package - Annotation - Returns annotation results
+  (isotope peaks, adducts and fragments)'
+homepage_url: http://workflow4metabolomics.org
+long_description: 'Part of the W4M project: http://workflow4metabolomics.org CAMERA:
+  http://bioconductor.org/packages/release/bioc/html/CAMERA.html Wrapper skript for
+  automatic annotation of isotope peaks, adducts and fragments for a (grouped) xcmsSet
+  xs. The function returns an xsAnnotate object. BEWARE: this tool don''t come with
+  its script. You will need to install the dedicated package_camara_w4m_script too'
+name: camera_annotate
+owner: lecorguille

galaxy/camera_annotate/Makefile

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+# USAGE: make [install|clean]
+
+# -------- VARIABLE --------
+
+OBJ=camera_annotate.tgz
+DEP=abims_CAMERA_annotateDiffreport.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
+

galaxy/camera_annotate/README.rst

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+
+Changelog/News
+--------------
+
+**Version  2.1.3 - 10/02/2016**
+
+- BUGFIX: better management of errors. Datasets remained green although the process failed
+
+- BUGFIX: the conversion into minutes of the retention time was applied to the diffreport outputs (several conditions)
+
+- IMPROVEMENT: when there are several conditions, the tool will generate individual datasets (tsv, pdf) instead of a zip file. The usual png (eic, boxplot) will from now be integrated in two pdf.
+
+- UPDATE: refactoring of internal management of inputs/outputs
+
+
+VERSION 2.1.0 - 09/10/2015**
+
+- BUGFIX: There was a bug with the CAMERA.annotate (generating a bad dataMatrix (intensities which don't match with the metabolites))
+
+
+VERSION 2.1.0 - 07/06/2015**
+
+- IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors.
+
+- IMPROVEMENT: parameter labels have changed to facilitate their reading.
+
+- UPDATE: merged with annotateDiffreport. Some parameters are dedicated to experiences with several conditions
+
+

galaxy/camera_annotate/planemo.sh

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+planemo shed_init -f --name=camera_annotate --owner=lecorguille --description="[W4M][GC-MS] CAMERA R Package - Preprocessing - Returns annotation results (isotope peaks, adducts and fragments)" --homepage_url="http://workflow4metabolomics.org" --long_description="Part of the W4M project: http://workflow4metabolomics.org CAMERA: http://bioconductor.org/packages/release/bioc/html/CAMERA.html Wrapper skript for automatic annotation of isotope peaks, adducts and fragments for a (grouped) xcmsSet xs. The function returns an xsAnnotate object. BEWARE: this tool don't come with its script. You will need to install the dedicated package_camara_w4m_script too" --category="Metabolomics"

galaxy/camera_annotate/repository_dependencies.xml

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+<?xml version="1.0"?>
+<repositories>
+	<repository name="rdata_camera_datatypes" owner="lecorguille" />
+	<repository name="rdata_xcms_datatypes" owner="lecorguille" />
+</repositories>

galaxy/camera_annotate/tool_dependencies.xml

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+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="3.1.2">
+        <repository name="package_r_3_1_2" owner="iuc" />
+    </package>
+    <package name="camera" version="1.22.0">
+        <repository name="package_r_camera_1_22_0" owner="lecorguille" />
+    </package>
+    <package name="camera_w4m_script" version="2.2.1">
+        <repository name="package_camera_w4m_script_2_2_1" owner="lecorguille" />
+    </package>
+    <package name="graphicsmagick" version="1.3.18">
+        <repository name="package_graphicsmagick_1_3" owner="iuc" />
+    </package>
+</tool_dependency>

galaxy/camera_combinexsannos/.shed.yml

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+categories: [Metabolomics]
+description: '[W4M][LC-MS] CAMERA R Package - Annotation - combinexsAnnos Check
+  CAMERA ion species annotation due to matching with opposite ion mode'
+homepage_url: http://workflow4metabolomics.org
+long_description: 'Part of the W4M project: http://workflow4metabolomics.org CAMERA:
+  http://bioconductor.org/packages/release/bioc/html/CAMERA.html This function check
+  annotations of ion species with the help of a sample from opposite ion mode. As
+  first step it searches for pseudospectra from the positive and the negative sample
+  within a retention time window. For every result the m/z differences between both
+  samples are matched against specific rules, which are combinations from pos. and
+  neg. ion species. As example M+H and M-H with a m/z difference of 2.014552. If two
+  ions matches such a difference, the ion annotations are changed (previous annotation
+  is wrong), confirmed or added. Returns the peaklist from one ion mode with recalculated
+  annotations. BEWARE: this tool don''t come with its script. You will need to install
+  the dedicated package_camara_w4m_script too'
+name: camera_combinexsannos
+owner: mmonsoor

galaxy/camera_combinexsannos/Makefile

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+# USAGE: make [install|clean]
+
+# -------- VARIABLE --------
+
+OBJ=camera_combinexsAnnos.tgz
+DEP=abims_CAMERA_combinexsAnnos.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
+

galaxy/camera_combinexsannos/README.rst

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+
+Changelog/News
+--------------
+
+**Version 2.0.3 - 10/02/2016**
+
+- BUGFIX: better management of errors. Datasets remained green although the process failed
+
+- UPDATE: refactoring of internal management of inputs/outputs
+
+
+**Version 2.0.1 - 07/06/2015**
+
+- IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors.
+
+- IMPROVEMENT: parameter labels have changed to facilitate their reading.
+
+
+**Version 2.0.0 - 09/06/2015**
+
+- NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode 
+

galaxy/camera_combinexsannos/abims_CAMERA_combinexsAnnos.xml

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+<tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.0.3">
+
+    <description>Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations.</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="1.22.0">camera</requirement>
+        <requirement type="package" version="2.2.0">camera_w4m_script</requirement>
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" level="fatal" />
+    </stdio>
+
+    <command><![CDATA[
+        CAMERA.r 
+        xfunction combinexsAnnos 
+        image_pos $image_pos 
+        image_neg $image_neg
+
+        variableMetadataOutput $variableMetadata
+
+        pos $pos tol $tol ruleset $ruleset convert_param $convert_param keep_meta $keep_meta
+        
+    ]]></command>
+
+    <inputs>
+        <param name="image_pos" type="data" label="Positive RData ion mode" format="rdata.camera.positive,rdata" help="output file from CAMERA.annotate using a positive polarity mode" />
+        <param name="image_neg" type="data" label="Negative RData ion mode" format="rdata.camera.negative,rdata" help="output file from CAMERA.annotate using a positive negative mode" />
+
+        <param name="pos" type="select" label="Returned peaklist polarity mode">
+            <option value="TRUE" selected="true">positive</option>
+            <option value="FALSE" >negative</option>
+        </param>
+
+        <param name="tol" type="integer" value="2" label="Retention time window in seconds" help="[pos] As first step it searches for pseudospectra from the positive and the negative sample within a retention time window" />
+        <param name="ruleset" type="text" value="1,1" label="Matrix of matching rules" help="[ruleset] Matrix of matching rules. By default, the matrix (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined!" />
+        <param name="convert_param" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) rtmed, rtmin and rtmax into minutes"/>
+        <param name="keep_meta" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Keep only the metabolites which match a difference "/>
+
+    </inputs>
+
+    <outputs>
+        <data name="variableMetadata" format="tabular" label="${image_pos.name[:-6]}.combinexsAnnos.variableMetadata.tsv" />
+        <!--
+        <data name="rdata" format="rdata" label="${image_pos.name[:-6]}.combinexsAnnos.Rdata" />
+        -->
+    </outputs>
+
+    <tests>
+        <test>
+            <!-- TODO: generer des vrais dataset pos et neg-->
+            <param name="image_pos" value="xset.group.retcor.group.fillPeaks.annotate.positive.Rdata"/>
+            <param name="image_neg" value="xset.group.retcor.group.fillPeaks.annotate.negative.Rdata"/>
+            <param name="pos" value="TRUE"/>
+            <param name="tol" value="2"/>
+            <param name="ruleset" value="1,1"/>
+            <output name="variableMetadata" file="xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" />
+        </test>
+    </tests>
+
+
+    <help><![CDATA[
+
+.. class:: infomark
+
+**Authors** Carsten Kuhl [email protected], Ralf Tautenhahn [email protected], Steffen Neumann sneumann@@ipb-halle.de
+
+.. class:: infomark
+
+**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton [email protected] - part of Workflow4Metabolomics.org [W4M]
+
+ | Contact [email protected] for any questions or concerns about the Galaxy implementation of this tool.
+
+---------------------------------------------------
+
+
+
+=======================
+Xcms.combinexsAnnos
+=======================
+
+-----------
+Description
+-----------
+
+**What it does?**
+
+This function check annotations of ion species with the help of a sample from opposite ion mode.
+As first step it searches for pseudospectra from the positive and the negative sample within a reten-
+tion time window. For every result the m/z differences between both samples are matched against
+specific rules, which are combinations from pos. and neg. ion species. As example M+H and M-H
+with a m/z difference of 2.014552. If two ions matches such a difference, the ion annotations are
+changed (previous annotation is wrong), confirmed or added. Returns the peaklist from one ion
+mode with recalculated annotations.
+
+**Details**
+
+Both xsAnnotate object should be full processed (grouping and annotation). Without previous anno-
+tation the resulting peaklist only includes annotation with matches peaks from both mode according
+to the rule(s). With ruleset=NULL the function only looks for M+H/M-H pairs. The ruleset is
+a two column matrix with includes rule indices from the rule table of both xsAnnotate objects.
+A ruleset (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and
+xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined!
+
+
+
+-----------------
+Workflow position
+-----------------
+
+
+**Upstream tools**
+
+========================= ======================= ===================== ==========
+Name                      Output file             Format                Parameter
+========================= ======================= ===================== ==========
+xcms.annotatediffreport   xset.annotate_POS.RData rdata.camera.positive RData file        			
+------------------------- ----------------------- --------------------- ----------
+xcms.annotatediffreport   xset.annotate_NEG.RData rdata.camera.positive RData file
+========================= ======================= ===================== ==========
+  
+**Downstream tools**
+
++---------------------------+-----------------------------------------+--------+
+| Name                      | Output file                             | Format |
++===========================+=========================================+========+
+|Batch_correction           |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
++---------------------------+-----------------------------------------+--------+
+|Filters                    |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
++---------------------------+-----------------------------------------+--------+
+|Univariate                 |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
++---------------------------+-----------------------------------------+--------+
+|Multivariate               |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
++---------------------------+-----------------------------------------+--------+
+
+
+
+The output file **xset.annotateDiffreport.variableMetadata.tsv** is a tabular file. You can continue your analysis using it in the following tools:
+    | Batch_correction
+    | Filters
+    | Univariate
+    | Multivariate PCA, PLS and OPLS
+
+
+**General schema of the metabolomic workflow**
+
+.. image:: combinexsannos_workflow.png
+
+
+-----------
+Input files
+-----------
+
++---------------------------+----------------------------+
+| Parameter : label         |   Format                   |
++===========================+============================+
+| Positive RData ion mode   |   rdata.camera.positive    |
++---------------------------+----------------------------+
+| Negative RData ion mode   |   rdata.camera.negative    |
++---------------------------+----------------------------+
+
+------------
+Output files
+------------
+
+xset.combinexsAnnos.variableMetadata.tsv
+
+    | A tabular file which is similar to the diffreport result , within additional columns containing the annotation results.
+    | For each metabolite (row) :
+    | the value of the intensity in each sample, fold, tstat, pvalue, anova, mzmed, mzmin, mzmax, rtmed, rtmin, rtmax, npeaks, isotopes, adduct, pcgroup and neg (or pos). Mode 
+
+xset.combinexsAnnos.Rdata
+
+    | Rdata file, that be used outside Galaxy in R.
+    
+
+---------------------------------------------------
+
+---------------
+Working example
+---------------
+
+Input files
+-----------
+
+    | Positive RData ion mode -> **POS.xset.annotateDiffreport.RData**
+    | Negative RData ion mode -> **NEG.xset.annotateDiffreport.RData**
+
+Parameters
+----------
+
+    | pos -> **positive**
+    | tol -> **2 (default)**
+    | ruleset -> **1,1 (default)**
+
+Output files
+------------
+
+**Example of an xset.combinexsAnnos.variableMetadata.tsv output:**
+
+.. image:: combinexsannos_variableMetadata.png
+
+
+---------------------------------------------------
+
+Changelog/News
+--------------
+
+**Version 2.0.3 - 10/02/2016**
+
+- BUGFIX: better management of errors. Datasets remained green although the process failed
+
+- UPDATE: refactoring of internal management of inputs/outputs
+
+
+**Version 2.0.1 - 07/06/2015**
+
+- IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors.
+
+- IMPROVEMENT: parameter labels have changed to facilitate their reading.
+
+
+**Version 2.0.0 - 09/06/2015**
+
+- NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode 
+
+
+    ]]></help>
+
+    <citations>
+        <citation type="doi"> 10.1021/ac202450g</citation>
+        <citation type="doi">10.1093/bioinformatics/btu813</citation>
+    </citations>
+
+
+</tool>
+
+

galaxy/camera_combinexsannos/planemo.sh

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+planemo shed_init -f --name=camera_combinexsannos --owner=lecorguille --description="[W4M][GC-MS] CAMERA R Package - Preprocessing - combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode" --homepage_url="http://workflow4metabolomics.org" --long_description="Part of the W4M project: http://workflow4metabolomics.org CAMERA: http://bioconductor.org/packages/release/bioc/html/CAMERA.html This function check annotations of ion species with the help of a sample from opposite ion mode. As first step it searches for pseudospectra from the positive and the negative sample within a retention time window. For every result the m/z differences between both samples are matched against specific rules, which are combinations from pos. and neg. ion species. As example M+H and M-H with a m/z difference of 2.014552. If two ions matches such a difference, the ion annotations are changed (previous annotation is wrong), confirmed or added. Returns the peaklist from one ion mode with recalculated annotations. BEWARE: this tool don't come with its script. You will need to install the dedicated package_camara_w4m_script too" --category="Metabolomics"