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comparison Marea/marea.xml @ 31:944e15aa970a draft

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author bimib
date Tue, 15 Oct 2019 12:22:43 -0400
parents 9fcb0e8d6d47
children b795e3e163e0
comparison
equal deleted inserted replaced
30:e88efefbd015 31:944e15aa970a
1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.2"> 1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.3">
2 <description></description> 2 <description></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>
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 #if $advanced.choice == 'true': 25
26 --none ${advanced.None}
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
40 --tool_dir $__tool_directory__ 26 --tool_dir $__tool_directory__
41 --option $cond.type_selector 27 --option $cond.type_selector
42 --out_log $log 28 --out_log $log
43 29
44 #if $cond.type_selector == 'datasets': 30 #if $cond.type_selector == 'datasets':
48 #end for 34 #end for
49 --names 35 --names
50 #for $data in $cond.input_Datasets: 36 #for $data in $cond.input_Datasets:
51 ${data.input_name} 37 ${data.input_name}
52 #end for 38 #end for
39 #if $cond.advanced.choice == 'true':
40 --none ${cond.advanced.None}
41 --pValue ${cond.advanced.pValue}
42 --fChange ${cond.advanced.fChange}
43 --generate_svg ${cond.advanced.generateSvg}
44 --generate_pdf ${cond.advanced.generatePdf}
45 --generate_ras ${cond.advanced.generateRas}
46 #else
47 --none true
48 --pValue 0.05
49 --fChange 1.5
50 --generate_svg false
51 --generate_pdf true
52 --generate_ras false
53 #end if
53 #elif $cond.type_selector == 'dataset_class': 54 #elif $cond.type_selector == 'dataset_class':
54 --input_data ${input_data} 55 --input_data ${input_data}
55 --input_class ${input_class} 56 --input_class ${input_class}
57 #if $cond.advanced.choice == 'true':
58 --none ${cond.advanced.None}
59 --pValue ${cond.advanced.pValue}
60 --fChange ${cond.advanced.fChange}
61 --generate_svg ${cond.advanced.generateSvg}
62 --generate_pdf ${cond.advanced.generatePdf}
63 --generate_ras ${cond.advanced.generateRas}
64 #else
65 --none true
66 --pValue 0.05
67 --fChange 1.5
68 --generate_svg false
69 --generate_pdf true
70 --generate_ras false
71 #end if
56 #end if 72 #end if
57 #if $cond.type_selector == 'datasets_rasonly': 73 #if $cond.type_selector == 'datasets_rasonly':
58 --input_datas ${input_Datasets} 74 --input_datas ${input_Datasets}
59 --single_ras_file $ras_single 75 --single_ras_file $ras_single
76 --none ${cond.advanced.None}
60 #end if 77 #end if
61 ]]> 78 ]]>
62 </command> 79 </command>
63 80
64 <inputs> 81 <inputs>
92 <when value="datasets"> 109 <when value="datasets">
93 <repeat name="input_Datasets" title="RNAseq" min="2"> 110 <repeat name="input_Datasets" title="RNAseq" min="2">
94 <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" /> 111 <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
95 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" /> 112 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
96 </repeat> 113 </repeat>
114 <conditional name="advanced">
115 <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.">
116 <option value="true" selected="true">No</option>
117 <option value="false">Yes</option>
118 </param>
119 <when value="false">
120 </when>
121 <when value="true">
122 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
123 <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />
124 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
125 <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?" />
126 <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?" />
127 <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" />
128 </when>
129 </conditional>
97 </when> 130 </when>
98 <when value="datasets_rasonly"> 131 <when value="datasets_rasonly">
99 <param name="input_Datasets" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" /> 132 <param name="input_Datasets" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
133 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
134 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
100 </when> 135 </when>
101 <when value="dataset_class"> 136 <when value="dataset_class">
102 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" /> 137 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
103 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" /> 138 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
139 <conditional name="advanced">
140 <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.">
141 <option value="true" selected="true">No</option>
142 <option value="false">Yes</option>
143 </param>
144 <when value="false">
145 </when>
146 <when value="true">
147 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
148 <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />
149 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
150 <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?" />
151 <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?" />
152 <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" />
153 </when>
154 </conditional>
104 </when> 155 </when>
105 </conditional> 156 </conditional>
106 157
158
107 159
108 <!--TODO: NASCONDERE ADVANCED SE RAS ONLY--> 160
109
110 <conditional name="advanced">
111 <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.">
112 <option value="true" selected="true">No</option>
113 <option value="false">Yes</option>
114 </param>
115 <when value="false">
116 </when>
117 <when value="true">
118 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
119 <param name="pValue" argument="--pValue" type="float" size="20" value="0.05" max="1" min="0" label="P-value threshold:" help="min value 0" />
120 <param name="fChange" argument="--fChange" type="float" size="20" value="1.5" min="1" label="Fold-Change threshold:" help="min value 1" />
121 <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?" />
122 <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?" />
123 <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" />
124 </when>
125 </conditional>
126 </inputs> 161 </inputs>
127 162
128 <outputs> 163 <outputs>
129 <data format="txt" name="log" label="${tool.name} - Log" /> 164 <data format="txt" name="log" label="MaREA - Log" />
130 <data format="tabular" name="ras_single" label="${tool.name} - RAS"> 165 <data format="tabular" name="ras_single" label="MaREA - RAS - ${cond.input_name}">
131 <filter>cond['type_selector'] == "datasets_rasonly"</filter> 166 <filter>cond['type_selector'] == "datasets_rasonly"</filter>
132 </data> 167 </data>
133 <collection name="results" type="list" label="${tool.name} - Results"> 168 <collection name="results" type="list" label="MaREA - Results">
134 <filter>cond['type_selector'] == "datasets" or cond['type_selector'] == "dataset_class"</filter> 169 <filter>cond['type_selector'] == "datasets" or cond['type_selector'] == "dataset_class"</filter>
135 <discover_datasets pattern="__name_and_ext__" directory="result"/> 170 <discover_datasets pattern="__name_and_ext__" directory="result"/>
136 </collection> 171 </collection>
137 <collection name="ras" type="list" label="${tool.name} - RAS list" format_source="tabular"> 172 <collection name="ras" type="list" label="MaREA - RAS list" format_source="tabular">
138 <filter>advanced['choice'] and advanced['generateRas']</filter> 173 <filter>cond['type_selector'] != "datasets_rasonly" and cond['advanced']['choice'] and cond['advanced']['generateRas']</filter>
139 <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/> 174 <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/>
140 </collection> 175 </collection>
141 176
142 </outputs> 177 </outputs>
143 <tests> 178 <tests>