--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/groupCorr.xml	Sun Nov 24 21:29:48 2024 +0000
@@ -0,0 +1,176 @@
+<tool id="CAMERA_groupCorr" name="CAMERA.groupCorr" version="0.1.0+camera@TOOL_VERSION@-galaxy@VERSION_SUFFIX@" profile="23.0">
+
+    <description>EIC correlation grouping of LC/ESI-MS data</description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements"/>
+
+    <required_files>
+        <include type="literal" path="CAMERA_groupCorr.R"/>
+        <include type="literal" path="lib.r"/>
+    </required_files>
+
+    <command detect_errors="exit_code"><![CDATA[
+		@COMMAND_RSCRIPT@CAMERA_groupCorr.R
+		image '$image'
+		cor_eic_th $cor_eic_th
+		pval $pval
+		graphMethod $graphMethod
+		calcIso $calcIso
+		calcCiS $calcCiS
+		calcCaS $calcCaS
+
+        #if $psg_list_block.psg_list_select == "FALSE":
+            psg_list NULL
+        #else
+            psg_list $psg_list
+        #end if
+        
+		cor_exp_th $cor_exp_th
+		intval $intval
+		numDigitsMZ $numDigitsMZ
+		numDigitsRT $numDigitsRT
+		convertRTMinute $convertRTMinute
+
+        @COMMAND_FILE_LOAD@
+		]]>
+    </command>
+
+    <inputs>
+        <param name="image" type="data" label="RData file" format="rdata" help="output file from another function xcms (fillPeaks)" />
+        <param name="cor_eic_th" type="float" value="0.75" max="1" min="0" label="Correlation threshold (0..1)" />
+        <param name="pval" type="float" value="0.05" max="1" min="0" label="Significant correlation threshold" />
+        <param name="graphMethod" type="select" label="Method selection for grouping peaks after correlation analysis into pseudospectra">
+            <option value="hcs" selected="true">hcs</option>
+            <option value="lpc">lpc</option>
+        </param>
+        <param name="calcIso" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Use isotopic relationship for peak grouping" />
+        <param name="calcCiS" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Use correlation inside samples for peak grouping" />
+        <param name="calcCaS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Use correlation across samples for peak grouping" />
+        <param name="cor_exp_th" type="float" value="0.75" max="1" min="0" label="Threshold for intensity correlations across samples (0..1)" />
+        <param name="intval" type="select" label="Method selection for grouping peaks after correlation analysis into pseudospectra">
+            <option value="into" selected="true">into</option>
+            <option value="maxo">maxo</option>
+            <option value="intb">intb</option>
+            <!-- <option value="intf">intf</option>
+                <option value="maxf">maxf</option>
+            <option value="area">area</option> -->
+        </param>
+        <conditional name="psg_list_block">
+            <param name="psg_list_select" type="select" label="Use a personal psg_list">
+                <option value="TRUE">TRUE</option>
+                <option value="FALSE" selected="true">FALSE</option>
+            </param>
+            <when value="FALSE">
+                <!--<param name="psg_list" type="text" value="NULL" label="No psg_list" optional="true" />-->
+            </when>
+            <when value="TRUE">
+                <param name="psg_list" type="text" optional="true" label="Pseudospectra indices (optional)" help="Provide a comma-separated list of pseudospectra indices (e.g. 1,2,3)." />
+            </when>
+        </conditional>
+        <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert seconds to minutes when exporting tsv" />
+        <param name="numDigitsMZ" type="integer" value="4" max="4" min="0" label="Number of digits for MZ values (namecustom)" />
+        <param name="numDigitsRT" type="integer" value="4" max="4" min="0" label="Number of digits for RT values (namecustom)" />
+        <expand macro="input_file_load"/>
+    </inputs>
+    <outputs>
+        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.groupCorr.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" />
+        <data name="camera_groupCorr_rdata" format="rdata" label="${image.name[:-6]}.groupCorr.RData" from_work_dir="camera_groupCorr.RData" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="image" value="xset.merged.group.retcor.group.fillPeaks.fwhm.RData" />
+            <!--<param name="cor_eic_th" value="0.75" />
+            <param name="pval" value="0.05" />
+            <param name="graphMethod" value="hcs" />
+            <param name="calcIso" value="FALSE" />
+            <param name="calcCiS" value="TRUE" />
+            <param name="calcCaS" value="FALSE" />
+            <param name="cor_exp_th" value="0.75" />
+            <param name="intval" value="into" />-->
+            <expand macro="test_file_load_faahKO_15"/>
+            <output name="variableMetadata" file="xset.merged.group.retcor.group.fillPeaks.fwhm.groupCorr.variableMetadata.tsv" />
+            <output name="camera_groupCorr_rdata" value="xset.merged.group.retcor.group.fillPeaks.fwhm.groupCorr.RData" compare="sim_size" delta="5000" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+================
+CAMERA.groupCorr
+================
+
+-----------
+Description
+-----------
+
+.. _link: https://bioconductor.org/packages/release/bioc/manuals/CAMERA/man/CAMERA.pdf
+
+Peak grouping after correlation information into pseudospectrum groups for an xsAnnotate object.
+Return an xsAnnotate object with grouping information. Click on the link to see the "Reference Manual" : link_ .
+
+---------------------------------------------------
+
+---------
+Arguments
+---------
+
++----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
+| Variables      | Descriptions                                                                                                                                |
++================+=============================================================================================================================================+
+| object         | the xsAnnotate object                                                                                                                       |
++----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
+| cor_eic_th     | Correlation threshold for EIC correlation                                                                                                   |
++----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
+| pval           | p-value threshold for testing correlation of significance                                                                                   |
++----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
+| graphMethod    | Clustering method for resulting correlation graph. See calcPC for more details.                                                             |
++----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
+| calcIso        | Include isotope detection information for graph clustering                                                                                  |
++----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
+| calcCiS        | Calculate correlation inside samples                                                                                                        |
++----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
+| calcCaS        | Calculate correlation across samples                                                                                                        |
++----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
+| psg_list       | Vector of pseudospectra indices. The correlation analysis will be only done for those groups                                                |
++----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
+| xraw           | Optional xcmsRaw object, which should be used for raw data extraction                                                                       |
++----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
+| cor_exp_th     | Threshold for intensity correlations across samples                                                                                         |
++----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
+| intval         | Selection of the intensity values (such as "into") that should be used in the correlation analysis. See getPeaklist for all allowed values. |
++----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
+
+---------------------------------------------------
+
+------------------------------------------
+General schema of the metabolomic workflow
+------------------------------------------
+
+.. image:: groupCorr.png
+
+---------------------------------------------------
+
+-------
+Details
+-------
+
+The algorithm calculates different informations for group peaks into so called pseudospectra. This pseudospectra contains peaks, with have a high correlation between each other. So far three different kind of information are available. Correlation of intensities across samples (need more than 3 samples), EIC correlation between peaks inside a sample and additional the informationen about recognized isotope cluster can be included. After calculation of all these informations, they are combined as edge value into a graph object. A following graph clustering algorithm separate the peaks (nodes in the graph) into the pseudospectra.
+
+---------------------------------------------------
+
+--------------
+Changelog/News
+--------------
+
+.. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS
+
+@HELP_CAMERA_SUITE@
+
+]]>    </help>
+
+    <expand macro="citation"/>
+    <expand macro="creator"/>
+</tool>