| Previous changeset 31:944e15aa970a (2019-10-15) Next changeset 33:abf0bfe01c78 (2019-10-16) |
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Commit message:
bug fix |
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modified:
Marea/marea.xml |
| b |
| diff -r 944e15aa970a -r b795e3e163e0 Marea/marea.xml --- a/Marea/marea.xml Tue Oct 15 12:22:43 2019 -0400 +++ b/Marea/marea.xml Wed Oct 16 07:12:37 2019 -0400 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.3">\n+<tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.4">\n <description></description>\n <macros>\n <import>marea_macros.xml</import>\n@@ -22,11 +22,11 @@\n --custom_map $cond_rule.cond_map.Custom_map\n #end if\n #end if\n-\t\n+\n \t--tool_dir $__tool_directory__\n \t--option $cond.type_selector\n- --out_log $log\t\t\n-\t\n+ --out_log $log\n+\n #if $cond.type_selector == \'datasets\':\n --input_datas\n #for $data in $cond.input_Datasets:\n@@ -43,7 +43,7 @@\n \t \t--generate_svg ${cond.advanced.generateSvg}\n \t \t--generate_pdf ${cond.advanced.generatePdf}\n \t --generate_ras ${cond.advanced.generateRas}\n-\t#else \n+\t#else\n \t --none true\n \t --pValue 0.05\n \t --fChange 1.5\n@@ -61,7 +61,7 @@\n \t --generate_svg ${cond.advanced.generateSvg}\n \t --generate_pdf ${cond.advanced.generatePdf}\n \t --generate_ras ${cond.advanced.generateRas}\n-\t#else \n+\t#else\n \t --none true\n \t --pValue 0.05\n \t --fChange 1.5\n@@ -73,7 +73,7 @@\n #if $cond.type_selector == \'datasets_rasonly\':\n --input_datas ${input_Datasets}\n --single_ras_file $ras_single\n- --none ${cond.advanced.None}\n+ --none ${None}\n #end if\n ]]>\n </command>\n@@ -108,7 +108,7 @@\n </param>\n <when value="datasets">\n <repeat name="input_Datasets" title="RNAseq" min="2">\n- <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />\t\n+ <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />\n <param name="input_name" argument="--names" type="text" label="Dataset\'s name:" value="Dataset" help="Default: Dataset" />\n </repeat>\n <conditional name="advanced">\n@@ -119,19 +119,19 @@\n \t\t\t\t\t<when value="false">\n \t\t\t\t\t</when>\n \t\t\t\t\t<when value="true">\n-\t\t \t\t\t<param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> \n+\t\t \t\t\t<param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />\n \t\t \t\t\t<param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />\n \t\t \t\t\t<param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />\n \t\t \t\t\t<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?" />\n-\t\t \t\t\t<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?" />\t\n-\t\t \t\t\t<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" />\t\t\n+\t\t \t\t\t<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?" />\n+\t\t \t\t\t<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" />\n \t\t\t\t\t</when>\n \t</conditional>\n </when>\n <when value="datasets_rasonly">\n <param name="input_Datasets" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />\n '..b'ype="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> \n+ <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />\n </when>\n <when value="dataset_class">\n <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />\n@@ -144,20 +144,20 @@\n \t\t\t\t\t<when value="false">\n \t\t\t\t\t</when>\n \t\t\t\t\t<when value="true">\n-\t\t \t\t\t<param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> \n+\t\t \t\t\t<param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />\n \t\t \t\t\t<param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />\n \t\t \t\t\t<param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />\n \t\t \t\t\t<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?" />\n-\t\t \t\t\t<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?" />\t\n-\t\t \t\t\t<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" />\t\t\n+\t\t \t\t\t<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?" />\n+\t\t \t\t\t<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" />\n \t\t\t\t\t</when>\n \t</conditional>\n </when>\n </conditional>\n- \n- \n- \n-\t\n+\n+\n+\n+\n </inputs>\n \n <outputs>\n@@ -173,7 +173,7 @@\n \t <filter>cond[\'type_selector\'] != "datasets_rasonly" and cond[\'advanced\'][\'choice\'] and cond[\'advanced\'][\'generateRas\']</filter>\n \t <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/>\n \t</collection>\n-\t\n+\n </outputs>\n <tests>\n <test>\n@@ -189,7 +189,7 @@\n \n 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.\n \n-Accepted files are: \n+Accepted files are:\n - 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*");\n - option 2) one RNA dataset and one class-file specifying the class/condition each sample belongs to.\n \n@@ -225,7 +225,7 @@\n \n **"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option:\n \n-RNA-seq Dataset 1:\t\t\t\t\t\t\n+RNA-seq Dataset 1:\n \n @DATASET_EXEMPLE1@\n \n@@ -241,14 +241,14 @@\n \n Class-file:\n \n-+------------+------------+ \n-| Patient_ID | class | \n-+============+============+ \n-| TCGAAA3529 | MSI | \n-+------------+------------+ \n-| TCGAA62671 | MSS | \n-+------------+------------+ \n-| TCGAA62672 | MSI | \n++------------+------------+\n+| Patient_ID | class |\n++============+============+\n+| TCGAAA3529 | MSI |\n++------------+------------+\n+| TCGAA62671 | MSS |\n++------------+------------+\n+| TCGAA62672 | MSI |\n +------------+------------+\n \n |\n@@ -271,4 +271,3 @@\n </help>\n <expand macro="citations" />\n </tool>\n-\t\n' |