Mercurial > repos > bimib > marea
diff Marea/marea.xml @ 33:abf0bfe01c78 draft
Uploaded
| author | bimib |
|---|---|
| date | Wed, 16 Oct 2019 16:25:56 -0400 |
| parents | b795e3e163e0 |
| children | 1a97d1537623 |
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--- a/Marea/marea.xml Wed Oct 16 07:12:37 2019 -0400 +++ b/Marea/marea.xml Wed Oct 16 16:25:56 2019 -0400 @@ -22,11 +22,11 @@ --custom_map $cond_rule.cond_map.Custom_map #end if #end if - + --tool_dir $__tool_directory__ --option $cond.type_selector - --out_log $log - + --out_log $log + #if $cond.type_selector == 'datasets': --input_datas #for $data in $cond.input_Datasets: @@ -43,7 +43,7 @@ --generate_svg ${cond.advanced.generateSvg} --generate_pdf ${cond.advanced.generatePdf} --generate_ras ${cond.advanced.generateRas} - #else + #else --none true --pValue 0.05 --fChange 1.5 @@ -61,7 +61,7 @@ --generate_svg ${cond.advanced.generateSvg} --generate_pdf ${cond.advanced.generatePdf} --generate_ras ${cond.advanced.generateRas} - #else + #else --none true --pValue 0.05 --fChange 1.5 @@ -73,7 +73,7 @@ #if $cond.type_selector == 'datasets_rasonly': --input_datas ${input_Datasets} --single_ras_file $ras_single - --none ${None} + --none ${cond.None} #end if ]]> </command> @@ -108,56 +108,56 @@ </param> <when value="datasets"> <repeat name="input_Datasets" title="RNAseq" min="2"> - <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" /> + <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" /> <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" /> </repeat> <conditional name="advanced"> - <param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom rules for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps."> + <param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom parameters for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps."> <option value="true" selected="true">No</option> <option value="false">Yes</option> </param> <when value="false"> </when> <when value="true"> - <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> + <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" /> <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" /> <param name="generateSvg" argument="--generateSvg" type="boolean" checked="false" label="Generate SVG map" help="should the program generate an editable svg map of the processes?" /> - <param name="generatePdf" argument="--generatePdf" type="boolean" checked="true" label="Generate PDF map" help="should the program return a non editable (but displayble) pdf map of the processes?" /> - <param name="generateRas" argument="--generateRas" type="boolean" checked="false" label="Generate Reaction Activity Score for each table" help="Generate Reaction Activity Score for each table" /> + <param name="generatePdf" argument="--generatePdf" type="boolean" checked="true" label="Generate PDF map" help="should the program return a non editable (but displayble) pdf map of the processes?" /> + <param name="generateRas" argument="--generateRas" type="boolean" checked="false" label="Generate Reaction Activity Score for each table" help="Generate Reaction Activity Score for each table" /> </when> </conditional> </when> <when value="datasets_rasonly"> <param name="input_Datasets" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" /> <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" /> - <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> + <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> </when> <when value="dataset_class"> <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" /> <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" /> <conditional name="advanced"> - <param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom rules for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps."> + <param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom parameters for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps."> <option value="true" selected="true">No</option> <option value="false">Yes</option> </param> <when value="false"> </when> <when value="true"> - <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> + <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" /> <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" /> <param name="generateSvg" argument="--generateSvg" type="boolean" checked="false" label="Generate SVG map" help="should the program generate an editable svg map of the processes?" /> - <param name="generatePdf" argument="--generatePdf" type="boolean" checked="true" label="Generate PDF map" help="should the program return a non editable (but displayble) pdf map of the processes?" /> - <param name="generateRas" argument="--generateRas" type="boolean" checked="false" label="Generate Reaction Activity Score for each table" help="Generate Reaction Activity Score for each table" /> + <param name="generatePdf" argument="--generatePdf" type="boolean" checked="true" label="Generate PDF map" help="should the program return a non editable (but displayble) pdf map of the processes?" /> + <param name="generateRas" argument="--generateRas" type="boolean" checked="false" label="Generate Reaction Activity Score for each table" help="Generate Reaction Activity Score for each table" /> </when> </conditional> </when> </conditional> - - - - + + + + </inputs> <outputs> @@ -173,7 +173,7 @@ <filter>cond['type_selector'] != "datasets_rasonly" and cond['advanced']['choice'] and cond['advanced']['generateRas']</filter> <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/> </collection> - + </outputs> <tests> <test> @@ -189,7 +189,7 @@ This tool analyzes RNA-seq dataset(s) as described in Graudenzi et al."`MaREA`_: Metabolic feature extraction, enrichment and visualization of RNAseq data" bioRxiv (2018): 248724. -Accepted files are: +Accepted files are: - option 1) two or more RNA-seq datasets, each referring to samples in a given condition/class. The user can specify a label for each class (as e.g. "*classA*" and "*classB*"); - option 2) one RNA dataset and one class-file specifying the class/condition each sample belongs to. @@ -225,7 +225,7 @@ **"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option: -RNA-seq Dataset 1: +RNA-seq Dataset 1: @DATASET_EXEMPLE1@ @@ -241,14 +241,14 @@ Class-file: -+------------+------------+ -| Patient_ID | class | -+============+============+ -| TCGAAA3529 | MSI | -+------------+------------+ -| TCGAA62671 | MSS | -+------------+------------+ -| TCGAA62672 | MSI | ++------------+------------+ +| Patient_ID | class | ++============+============+ +| TCGAAA3529 | MSI | ++------------+------------+ +| TCGAA62671 | MSS | ++------------+------------+ +| TCGAA62672 | MSI | +------------+------------+ | @@ -271,3 +271,4 @@ </help> <expand macro="citations" /> </tool> +