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comparison Marea/marea.xml @ 16:c71ac0bb12de draft

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Uploaded
author bimib
date Tue, 01 Oct 2019 06:05:13 -0400
parents e96f3b85e5a0
children 100c116d0d25
comparison
equal deleted inserted replaced
15:d0e7f14b773f 16:c71ac0bb12de
1 <tool id="MaREA" name="Metabolic Enrichment Analysis" version="1.0.0"> 1 <tool id="MaREA" name="Metabolic Enrichment Analysis" version="1.0.1">
2 <description>for Galaxy</description> 2 <description>for Galaxy - 1.0.1</description>
3 <macros> 3 <macros>
4 <import>marea_macros.xml</import> 4 <import>marea_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="0.23.0">pandas</requirement> 7 <requirement type="package" version="0.23.0">pandas</requirement>
20 --yes_no ${cond_rule.cond_map.yes_no} 20 --yes_no ${cond_rule.cond_map.yes_no}
21 #if $cond_rule.cond_map.yes_no == 'yes': 21 #if $cond_rule.cond_map.yes_no == 'yes':
22 --custom_map $cond_rule.cond_map.Custom_map 22 --custom_map $cond_rule.cond_map.Custom_map
23 #end if 23 #end if
24 #end if 24 #end if
25 --none $None 25 #if $advanced.choice == 'true':
26 --pValue $pValue 26 --none ${advanced.None}
27 --fChange $fChange 27 --pValue ${advanced.pValue}
28 --fChange ${advanced.fChange}
29 --generate_svg ${advanced.generateSvg}
30 --generate_pdf ${advanced.generatePdf}
31 --generate_ras ${advanced.generateRas}
32 #else
33 --none true
34 --pValue 0.05
35 --fChange 1.5
36 --generate_svg false
37 --generate_pdf true
38 --generate_ras false
39 #end if
28 --tool_dir $__tool_directory__ 40 --tool_dir $__tool_directory__
29 --option $cond.type_selector 41 --option $cond.type_selector
30 --out_log $log 42 --out_log $log
43
31 #if $cond.type_selector == 'datasets': 44 #if $cond.type_selector == 'datasets':
32 --input_datas 45 --input_datas
33 #for $data in $cond.input_Datasets: 46 #for $data in $cond.input_Datasets:
34 ${data.input} 47 ${data.input}
35 #end for 48 #end for
72 <option value="dataset_class">RNAseq of all samples + sample group specification</option> 85 <option value="dataset_class">RNAseq of all samples + sample group specification</option>
73 </param> 86 </param>
74 <when value="datasets"> 87 <when value="datasets">
75 <repeat name="input_Datasets" title="RNAseq" min="2"> 88 <repeat name="input_Datasets" title="RNAseq" min="2">
76 <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" /> 89 <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
77 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Defalut: Dataset" /> 90 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
78 </repeat> 91 </repeat>
79 </when> 92 </when>
80 <when value="dataset_class"> 93 <when value="dataset_class">
81 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" /> 94 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
82 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" /> 95 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
83 </when> 96 </when>
84 </conditional> 97 </conditional>
85 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> 98
86 <param name="pValue" argument="--pValue" type="float" size="20" value="0.05" max="1" min="0" label="P-value threshold:" help="min value 0" /> 99 <conditional name="advanced">
87 <param name="fChange" argument="--fChange" type="float" size="20" value="1.5" min="1" label="Fold-Change threshold:" help="min value 1" /> 100 <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.">
101 <option value="true" selected="true">No</option>
102 <option value="false">Yes</option>
103 </param>
104 <when value="false">
105 </when>
106 <when value="true">
107 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
108 <param name="pValue" argument="--pValue" type="float" size="20" value="0.05" max="1" min="0" label="P-value threshold:" help="min value 0" />
109 <param name="fChange" argument="--fChange" type="float" size="20" value="1.5" min="1" label="Fold-Change threshold:" help="min value 1" />
110 <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?" />
111 <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?" />
112 <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" />
113 </when>
114 </conditional>
88 </inputs> 115 </inputs>
89 116
90 <outputs> 117 <outputs>
91 <data format="txt" name="log" label="Log" /> 118 <data format="txt" name="log" label="${tool.name} - Log" />
92 <collection name="map_svg" type="list" label="Graphical results (.svg)"> 119 <collection name="results" type="list" label="${tool.name} - Results">
93 <filter>(cond_rule['rules_selector'] == 'HMRcore') or ((cond_rule['rules_selector'] == 'Custom') and (cond_rule['cond_map']['yes_no'] == 'yes'))</filter> 120 <discover_datasets pattern="__name_and_ext__" directory="result"/>
94 <discover_datasets pattern="__name_and_ext__" directory="map_svg" />
95 </collection> 121 </collection>
96 <collection name="map_pdf" type="list" label="Graphical results (.pdf)"> 122 <collection name="ras" type="list" label="${tool.name} - RAS" format_source="tabular">
97 <filter>(cond_rule['rules_selector'] == 'HMRcore') or ((cond_rule['rules_selector'] == 'Custom') and (cond_rule['cond_map']['yes_no'] == 'yes'))</filter> 123 <filter>advanced['choice'] and advanced['generateRas']</filter>
98 <discover_datasets pattern="__name_and_ext__" directory="map_pdf" /> 124 <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/>
99 </collection> 125 </collection>
100 <collection name="table_out" type="list" label="Tabular results">
101 <discover_datasets pattern="__name_and_ext__" directory="table_out" />
102 </collection>
103 </outputs> 126 </outputs>
104 <tests> 127 <tests>
105 <test> 128 <test>
106 <param name="pValue" value="0.56"/> 129 <param name="pValue" value="0.56"/>
107 <output name="log" file="log.txt"/> 130 <output name="log" file="log.txt"/>