Mercurial > repos > melpetera > intensity_checks

changeset 4:49c36c54e0cf draft

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Uploaded
author melpetera
date Fri, 03 Jan 2020 11:09:05 -0500
parents bdee2c2c484b
children a31f3f802b2b
files Intchecks/README.md Intchecks/static/images/int_check.png Intchecks/wrapper_intensity_check.R Intchecks/xml_intensity_check.xml
diffstat 4 files changed, 121 insertions(+), 21 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Intchecks/README.md	Fri Jan 03 11:09:05 2020 -0500
@@ -0,0 +1,51 @@
+Intensity check
+=======
+
+Metadata
+-----------
+
+ * **@name**: Intensity check
+ * **@version**: 1.2.8
+ * **@authors**: Original code: Anthony Fernandes (PFEM - INRA) - Maintainer: Melanie Petera (PFEM - INRAE - MetaboHUB)
+ * **@init date**: 2018, September
+ * **@main usage**: This tool computes some statistical measures, number of missing values and mean fold change.
+
+ 
+Context
+-----------
+
+This tool is provided as one of the [Workflow4Metabolomics](http://workflow4metabolomics.org) Galaxy instance statistical tools. 
+W4M is a French infrastructure providing software tools to process, analyse and annotate metabolomics data. 
+
+User interface is based on the Galaxy platform (homepage: https://galaxyproject.org/). It is an open, web-based platform for data intensive biomedical research. 
+Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.
+
+ 
+Configuration
+-----------
+
+### Requirement:
+ * R software: version > 3.0.0 recommended
+ * Specific R libraries: 'batch' 
+
+
+Technical description
+-----------
+
+Main files:
+
+- Script_intensity_check.R: R function (core script)
+- wrapper_intensity_check.R: R script to link the main R function to inputs
+- xml_intensity_check.xml: XML wrapper (interface for Galaxy)
+
+
+Services provided
+-----------
+
+ * Help and support: support@workflow4metabolomics.org
+
+
+License
+-----------
+
+ * Cea Cnrs Inria Logiciel Libre License, version 2.1 (CECILL-2.1)
Binary file Intchecks/static/images/int_check.png has changed
--- a/Intchecks/wrapper_intensity_check.R	Fri Mar 08 09:07:12 2019 -0500
+++ b/Intchecks/wrapper_intensity_check.R	Fri Jan 03 11:09:05 2020 -0500
@@ -29,6 +29,12 @@
 
 if(length(args) < 7){ stop("NOT enough argument !!!") }
 
+cat('\nJob starting time:\n',format(Sys.time(), "%a %d %b %Y %X"),
+'\n\n--------------------------------------------------------------------', 
+'\nIntensity Check parameters:\n\n')
+print(args)
+cat('--------------------------------------------------------------------\n\n')
+
 class_col <- NULL
 test_fold <- NULL
 class1 <- NULL
@@ -55,24 +61,24 @@
 
 if(((args$method == "no_class")&&(args$chosen_stat == "None"))||
    ((args$method != "no_class") && (args$chosen_stat == "None") && (test_fold == "No"))){
-  err_no_option<- "You did not select any computational option. Program could not be executed."
+  err_no_option<- "You did not select any computational option. Program can not be executed."
   stop("\n- - - - - - - - -\n",err_no_option,"\n- - - - - - - - -\n")
 }
 
 
-#print args
-cat("\n-------------------------------\nIntensity Check parameters:\n\n")
-print(args)
-cat("--------------------------------\n")
-
 if(is.null(err_no_option)){
 
   intens_check(args$dataMatrix_in, args$sampleMetadata_in, args$variableMetadata_in, args$method, args$chosen_stat, 
              class_col, test_fold, class1, fold_frac, logarithm, args$variableMetadata_out, args$graphs_out)
 }
-  
+
+
+cat('\n--------------------------------------------------------------------',
+'\nInformation about R (version, Operating System, attached or loaded packages):\n\n')
 sessionInfo()
-cat("--------------------------------\n")
+cat('--------------------------------------------------------------------\n',
+'\nJob ending time:\n',format(Sys.time(), "%a %d %b %Y %X"))
+
 
 #delete the parameters to avoid the passage to the next tool in .RData image
 rm(args)
--- a/Intchecks/xml_intensity_check.xml	Fri Mar 08 09:07:12 2019 -0500
+++ b/Intchecks/xml_intensity_check.xml	Fri Jan 03 11:09:05 2020 -0500
@@ -1,7 +1,7 @@
-<tool id="intens_check" name="Intensity Check" version="1.2.1">
+<tool id="intens_check" name="Intensity Check" version="1.2.8">
 	<description>Statistical measures, number of missing values and mean fold change</description>
 	<requirements>
-	<requirement type="package" version="1.1_5">r-batch</requirement>
+	    <requirement type="package" version="1.1_5">r-batch</requirement>
 	</requirements>
 	<command interpreter="Rscript">
   
@@ -41,7 +41,7 @@
 	</command>
 
 	<inputs>
-		<param name="dataMatrix_in" type="data" label="Data Matrix file" help="" format="tabular" />
+		<param name="dataMatrix_in" type="data" label="Data matrix file" help="" format="tabular" />
 		<param name="sampleMetadata_in" type="data" label="Sample metadata file" help="" format="tabular" />
 		<param name="variableMetadata_in" type="data" label="Variable metadata file" help="" format="tabular" />
 		
@@ -128,12 +128,15 @@
 		<data name="graphs_out" label="IC_Graphs" format="pdf" />
 	</outputs>
 	
+	
+	
 	<help>
 
 .. class:: infomark
 
-**Authors** 
-  | Anthony Fernandes - PFEM ; INRA 
+**Author:** 
+Anthony Fernandes for original code (PFEM - INRA) 
+**Maintainer:** Melanie Petera (PFEM - INRAE - MetaboHUB)
 
 ---------------------------------------------------
 
@@ -142,19 +145,39 @@
 ========================
 
 -----------
+Description
+-----------
+
+This tool performs various metrics: mean fold change calculation, number and proportion of missing values, and mean, sd and decile calculation.
+You can choose to perform these metrics according to sample groups defined in the sample metadata file given as input. 
+
+ 
+-----------------
+Workflow position
+-----------------
+
+
+.. image:: int_check.png
+        :width: 800
+
+
+-----------
 Input files
 -----------
 
 +----------------------------+------------+
 | Parameter                  |   Format   |
 +============================+============+
-| 1 : Data Matrix file       |   tabular  |
+| 1 : Data matrix file       |   tabular  |
 +----------------------------+------------+
 | 2 : Sample metadata file   |   tabular  |
 +----------------------------+------------+
 | 3 : Variable metadata file |   tabular  |
 +----------------------------+------------+
 
+	| 
+
+
 ----------
 Parameters
 ----------
@@ -167,21 +190,21 @@
 	| In the case of two classes: "each class" and "one class" give the same results for statistical measures. We recommend to choose "one class" for mean fold change calculation in order to select the class you want to put as numerator or denominator (see below).
 	
 **Statistics**
-	|  Select the statistical measures you want to add in the variable metadata table. If the method is "each class" or "one class", you could choose no statistical measure if you only want to calculate the mean fold change (see below).
+	|  Select the statistical measures you want to add in the variable metadata table. If the method is "each class" or "one class", you can choose to leave this section blank if you only want to calculate the mean fold change (see below).
 
-**Class column**
+**Class column** (*only if "each class" or "one class"*)
 	| Select the class column in sample metadata table.
 
-**Selected class**
+**Selected class** (*only if "one class"*)
 	| If the method is "one class", specify it. Remaining samples will be named "Other".
 	
-**Calculate the mean fold change**
+**Calculate the mean fold change** (*only if "each class" or "one class"*)
 	| Choose if you want to calculate the mean fold change. If the method is "each class": mean fold change will be calculated for all combinations of classes. If the method is "one class": it will be calculated between the selected class (see above) and the remaining samples.
 	
-**Where should the class be placed for the mean fold change calculation?**	
+**Where should the class be placed for the mean fold change calculation?** (*only if "one class"*)
 	| If the method is "one class", choose "top" or "bottom" to put the selected class as numerator or denominator (respectively) for the mean fold change calculation.	
 	
-**Logarithm**
+**Logarithm** (*only if "each class" or "one class"*)
 	| Choose if you want to transform the mean fold change with a log2 or log10.
 	
 ------------
@@ -190,11 +213,31 @@
 
 **Variable metadata file**
 	| Contains the previous columns in variable metadata file and the new ones.
-	| In the column names for fold, the first class specified is the one used like numerator for the ratio.
+	| In the column names for fold, the first class specified is the one used as numerator in the ratio.
 	
 **Graphs file**
 	| Contains barplots with the proportion of NA considering classes and boxplots with the fold values.
 
+
+
+---------------------------------------------------
+
+----------------------
+Additional information
+----------------------
+
+
+.. class:: warningmark
+
+For more information about input files, refer to the corresponding "W4M HowTo" page:
+ | `W4M table format for Galaxy &lt;http://workflow4metabolomics.org/sites/workflow4metabolomics.org/files/files/w4m_TableFormatForGalaxy_150908.pdf&gt;`_
+ |
+
+
+
+
+
+
 	</help>