Mercurial > repos > melpetera > acorrf
diff ACF/analytic_correlation_filtration.xml @ 3:573520b2e3b0 draft default tip
Uploaded
| author | melpetera |
|---|---|
| date | Tue, 17 Dec 2019 10:47:31 +0000 |
| parents | bcf48aff1077 |
| children |
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--- a/ACF/analytic_correlation_filtration.xml Wed Oct 30 10:50:07 2019 -0400 +++ b/ACF/analytic_correlation_filtration.xml Tue Dec 17 10:47:31 2019 +0000 @@ -1,4 +1,4 @@ -<tool id="Analytic_correlation_filtration" name="Analytic correlation filtration" version="2019-06-20"> +<tool id="Analytic_correlation_filtration" name="Analytic correlation filtration" version="2019-10-31"> <description> : Detect analytic correlation among data and remove them. </description> @@ -19,6 +19,7 @@ #else: #if str($mass_file.liste.mass_list)=="true": #if str($rt_cond.rt_choice)=="true": + #if str($rt_cond.rt_choice)=="true": perl $__tool_directory__/Analytic_correlation_filtration.pl -f "$file_in" -m "$mass_file.liste.mass_file_in" -o 2 -d "$dataMatrix_in" -v "$variableMetadata_in" -rt "$rt_cond.rt_threshold" -mass "$mass_file.mass_threshold" #end if #if str($rt_cond.rt_choice)=="false": @@ -26,10 +27,20 @@ #end if #else #if str($rt_cond.rt_choice)=="true": - perl $__tool_directory__/Analytic_correlation_filtration.pl -f "$file_in" -m $__tool_directory__/data/default_list.csv -o 2 -d "$dataMatrix_in" -v "$variableMetadata_in" -rt "$rt_cond.rt_threshold" -mass "$mass_file.mass_threshold" + #if str($method_opt.method_selection)=="LC": + perl $__tool_directory__/Analytic_correlation_filtration.pl -f "$file_in" -m $__tool_directory__/data/default_list_LC.csv -o 2 -d "$dataMatrix_in" -v "$variableMetadata_in" -rt "$rt_cond.rt_threshold" -mass "$mass_file.mass_threshold" + #end if + #if str($method_opt.method_selection)=="GC": + perl $__tool_directory__/Analytic_correlation_filtration.pl -f "$file_in" -m $__tool_directory__/data/default_list_LC_GC.csv -o 2 -d "$dataMatrix_in" -v "$variableMetadata_in" -rt "$rt_cond.rt_threshold" -mass "$mass_file.mass_threshold" + #end if #end if #if str($rt_cond.rt_choice)=="false": - perl $__tool_directory__/Analytic_correlation_filtration.pl -f "$file_in" -m $__tool_directory__/data/default_list.csv -o 3 -d "$dataMatrix_in" -v "$variableMetadata_in" -mass "$mass_file.mass_threshold" + #if str($method_opt.method_selection)=="LC": + perl $__tool_directory__/Analytic_correlation_filtration.pl -f "$file_in" -m $__tool_directory__/data/default_list_LC.csv -o 3 -d "$dataMatrix_in" -v "$variableMetadata_in" -mass "$mass_file.mass_threshold" + #end if + #if str($method_opt.method_selection)=="GC": + perl $__tool_directory__/Analytic_correlation_filtration.pl -f "$file_in" -m $__tool_directory__/data/default_list_GC.csv -o 3 -d "$dataMatrix_in" -v "$variableMetadata_in" -mass "$mass_file.mass_threshold" + #end if #end if #end if #end if @@ -59,7 +70,12 @@ <conditional name="liste"> <param name="mass_list" checked="true" falsevalue="false" help="'YES' if you have your own list to upload; 'NO' if you want to use a default list" label="Do you have your own list of mass differences or do you want to use a default list ?" truevalue="true" type="boolean"/> <when value="false"> - + <conditional name="method_opt"> + <param name="method_selection" label="Are you analysing LC/MS or GC/MS data ?" type="select" display="radio" help=""> + <option value="LC">LC/MS</option> + <option value="GC">GC/MS</option> + </param> + </conditional> </when> <when value="true"> <param type="data" name="mass_file_in" format="tabular,csv" help="The file containing all your report and known mass differences (cf help for file example) " label="Mass differences table (format: tabular or csv) " />