Mercurial > repos > melpetera > acorrf
comparison ACF/analytic_correlation_filtration.xml @ 3:573520b2e3b0 draft default tip
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| author | melpetera |
|---|---|
| date | Tue, 17 Dec 2019 10:47:31 +0000 |
| parents | bcf48aff1077 |
| children |
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| 2:bcf48aff1077 | 3:573520b2e3b0 |
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| 1 <tool id="Analytic_correlation_filtration" name="Analytic correlation filtration" version="2019-06-20"> | 1 <tool id="Analytic_correlation_filtration" name="Analytic correlation filtration" version="2019-10-31"> |
| 2 <description> | 2 <description> |
| 3 : Detect analytic correlation among data and remove them. | 3 : Detect analytic correlation among data and remove them. |
| 4 </description> | 4 </description> |
| 5 | 5 |
| 6 | 6 |
| 17 perl $__tool_directory__/Analytic_correlation_filtration.pl -f "$file_in" -o 1 -d "$dataMatrix_in" -v "$variableMetadata_in" -rt "$rt_cond.rt_threshold" | 17 perl $__tool_directory__/Analytic_correlation_filtration.pl -f "$file_in" -o 1 -d "$dataMatrix_in" -v "$variableMetadata_in" -rt "$rt_cond.rt_threshold" |
| 18 #end if | 18 #end if |
| 19 #else: | 19 #else: |
| 20 #if str($mass_file.liste.mass_list)=="true": | 20 #if str($mass_file.liste.mass_list)=="true": |
| 21 #if str($rt_cond.rt_choice)=="true": | 21 #if str($rt_cond.rt_choice)=="true": |
| 22 #if str($rt_cond.rt_choice)=="true": | |
| 22 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" | 23 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 "$mass_file.mass_threshold" |
| 23 #end if | 24 #end if |
| 24 #if str($rt_cond.rt_choice)=="false": | 25 #if str($rt_cond.rt_choice)=="false": |
| 25 perl $__tool_directory__/Analytic_correlation_filtration.pl -f "$file_in" -m "$mass_file.liste.mass_file_in" -o 3 -d "$dataMatrix_in" -v "$variableMetadata_in" -mass "$mass_file.mass_threshold" | 26 perl $__tool_directory__/Analytic_correlation_filtration.pl -f "$file_in" -m "$mass_file.liste.mass_file_in" -o 3 -d "$dataMatrix_in" -v "$variableMetadata_in" -mass "$mass_file.mass_threshold" |
| 26 #end if | 27 #end if |
| 27 #else | 28 #else |
| 28 #if str($rt_cond.rt_choice)=="true": | 29 #if str($rt_cond.rt_choice)=="true": |
| 29 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 "$mass_file.mass_threshold" | 30 #if str($method_opt.method_selection)=="LC": |
| 31 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 "$mass_file.mass_threshold" | |
| 32 #end if | |
| 33 #if str($method_opt.method_selection)=="GC": | |
| 34 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 "$mass_file.mass_threshold" | |
| 35 #end if | |
| 30 #end if | 36 #end if |
| 31 #if str($rt_cond.rt_choice)=="false": | 37 #if str($rt_cond.rt_choice)=="false": |
| 32 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" | 38 #if str($method_opt.method_selection)=="LC": |
| 39 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" | |
| 40 #end if | |
| 41 #if str($method_opt.method_selection)=="GC": | |
| 42 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" | |
| 43 #end if | |
| 33 #end if | 44 #end if |
| 34 #end if | 45 #end if |
| 35 #end if | 46 #end if |
| 36 | 47 |
| 37 -r "$repres_opt.repres_opt_selector" | 48 -r "$repres_opt.repres_opt_selector" |
| 57 <param name="mass_choice" checked="true" falsevalue="false" help="'YES' if you want to take it into account; 'NO' if you don't want to take into account mass information" label="Do you want to take into account mass differences between 2 ions?" truevalue="true" type="boolean"/> | 68 <param name="mass_choice" checked="true" falsevalue="false" help="'YES' if you want to take it into account; 'NO' if you don't want to take into account mass information" label="Do you want to take into account mass differences between 2 ions?" truevalue="true" type="boolean"/> |
| 58 <when value="true"> | 69 <when value="true"> |
| 59 <conditional name="liste"> | 70 <conditional name="liste"> |
| 60 <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"/> | 71 <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"/> |
| 61 <when value="false"> | 72 <when value="false"> |
| 62 | 73 <conditional name="method_opt"> |
| 74 <param name="method_selection" label="Are you analysing LC/MS or GC/MS data ?" type="select" display="radio" help=""> | |
| 75 <option value="LC">LC/MS</option> | |
| 76 <option value="GC">GC/MS</option> | |
| 77 </param> | |
| 78 </conditional> | |
| 63 </when> | 79 </when> |
| 64 <when value="true"> | 80 <when value="true"> |
| 65 <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) " /> | 81 <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) " /> |
| 66 </when> | 82 </when> |
| 67 </conditional> | 83 </conditional> |