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comparison Marea/marea.xml @ 47:3af9d394367c draft

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author bimib
date Wed, 19 Feb 2020 10:44:52 -0500
parents 7b1971251c63
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46:5d5d01ef1d68 47:3af9d394367c
1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.6"> 1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.7">
2 <description></description> 2 <macros>
3 <macros> 3 <import>marea_macros.xml</import>
4 <import>marea_macros.xml</import> 4 </macros>
5 </macros> 5 <requirements>
6 <requirements> 6 <requirement type="package" version="0.23.0">pandas</requirement>
7 <requirement type="package" version="0.23.0">pandas</requirement> 7 <requirement type="package" version="1.1.0">scipy</requirement>
8 <requirement type="package" version="1.1.0">scipy</requirement> 8 <requirement type="package" version="0.10.1">cobra</requirement>
9 <requirement type="package" version="0.10.1">cobra</requirement> 9 <requirement type="package" version="4.2.1">lxml</requirement>
10 <requirement type="package" version="4.2.1">lxml</requirement> 10 <requirement type="package" version="0.8.1">svglib</requirement>
11 <requirement type="package" version="0.8.1">svglib</requirement> 11 <requirement type="package" version="3.4.0">reportlab</requirement>
12 <requirement type="package" version="3.4.0">reportlab</requirement> 12 </requirements>
13 </requirements> 13 <command detect_errors="exit_code">
14 <command detect_errors="exit_code"> 14 <![CDATA[
15 <![CDATA[
16 python $__tool_directory__/marea.py 15 python $__tool_directory__/marea.py
17 --rules_selector $cond_rule.rules_selector 16
18 #if $cond_rule.rules_selector == 'Custom':
19 --custom ${cond_rule.Custom_rules}
20 --yes_no ${cond_rule.cond_map.yes_no}
21 #if $cond_rule.cond_map.yes_no == 'yes':
22 --custom_map $cond_rule.cond_map.Custom_map
23 #end if
24 #end if
25
26 --tool_dir $__tool_directory__ 17 --tool_dir $__tool_directory__
27 --option $cond.type_selector 18 --option $cond.type_selector
28 --out_log $log 19 --out_log $log
29 20
30 #if $cond.type_selector == 'datasets': 21 #if $cond.type_selector == 'datasets':
34 #end for 25 #end for
35 --names 26 --names
36 #for $data in $cond.input_Datasets: 27 #for $data in $cond.input_Datasets:
37 ${data.input_name} 28 ${data.input_name}
38 #end for 29 #end for
30 --comparison ${cond.comparis.comparison}
39 #if $cond.advanced.choice == 'true': 31 #if $cond.advanced.choice == 'true':
40 --none ${cond.advanced.None} 32 --pValue ${cond.advanced.pValue}
41 --pValue ${cond.advanced.pValue} 33 --fChange ${cond.advanced.fChange}
42 --fChange ${cond.advanced.fChange} 34 --generate_svg ${cond.advanced.generateSvg}
43 --generate_svg ${cond.advanced.generateSvg} 35 --generate_pdf ${cond.advanced.generatePdf}
44 --generate_pdf ${cond.advanced.generatePdf} 36 #else
45 --generate_ras ${cond.advanced.generateRas} 37 --pValue 0.05
46 #else 38 --fChange 1.5
47 --none true 39 --generate_svg false
48 --pValue 0.05 40 --generate_pdf true
49 --fChange 1.5 41 --generate_ras false
50 --generate_svg false 42 #end if
51 --generate_pdf true
52 --generate_ras false
53 #end if
54 #elif $cond.type_selector == 'dataset_class': 43 #elif $cond.type_selector == 'dataset_class':
55 --input_data ${input_data} 44 --input_data ${input_data}
56 --input_class ${input_class} 45 --input_class ${input_class}
46 --comparison ${cond.comparis.comparison}
47 #if $cond.comparis.comparison == 'onevsmany'
48 --control ${cond.comparis.controlgroup}
49 #end if
57 #if $cond.advanced.choice == 'true': 50 #if $cond.advanced.choice == 'true':
58 --none ${cond.advanced.None} 51 --pValue ${cond.advanced.pValue}
59 --pValue ${cond.advanced.pValue} 52 --fChange ${cond.advanced.fChange}
60 --fChange ${cond.advanced.fChange} 53 --generate_svg ${cond.advanced.generateSvg}
61 --generate_svg ${cond.advanced.generateSvg} 54 --generate_pdf ${cond.advanced.generatePdf}
62 --generate_pdf ${cond.advanced.generatePdf} 55 #else
63 --generate_ras ${cond.advanced.generateRas} 56 --pValue 0.05
64 #else 57 --fChange 1.5
65 --none true 58 --generate_svg false
66 --pValue 0.05 59 --generate_pdf true
67 --fChange 1.5 60 #end if
68 --generate_svg false
69 --generate_pdf true
70 --generate_ras false
71 #end if
72 #end if
73 #if $cond.type_selector == 'datasets_rasonly':
74 --input_datas ${input_Datasets}
75 --single_ras_file $ras_single
76 --none ${cond.None}
77 #end if 61 #end if
78 ]]> 62 ]]>
79 </command> 63 </command>
80 64 <inputs>
81 <inputs> 65 <conditional name="cond">
82 <conditional name="cond_rule"> 66 <param name="type_selector" argument="--option" type="select" label="Input format:">
83 <expand macro="options"/> 67 <option value="datasets" selected="true">RAS of group 1 + RAS of group 2 + ... + RAS of group N</option>
84 <when value="HMRcore"> 68 <option value="dataset_class">RAS of all samples + sample group specification</option>
85 </when> 69 </param>
86 <when value="Recon"> 70 <when value="datasets">
87 </when> 71 <repeat name="input_Datasets" title="RAS dataset" min="2">
88 <when value="Custom"> 72 <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
89 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" /> 73 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
90 <conditional name="cond_map"> 74 </repeat>
91 <param name="yes_no" type="select" label="Custom map? (optional)"> 75 <conditional name="comparis">
92 <option value="no" selected="true">no</option> 76 <param name="comparison" argument="--comparison" type="select" label="Groups comparison:">
93 <option value="yes">yes</option> 77 <option value="manyvsmany" selected="true">One vs One</option>
94 </param> 78 <option value="onevsrest">One vs All</option>
95 <when value="yes"> 79 <option value="onevsmany">One vs Control</option>
96 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/> 80 </param>
97 </when> 81 <when value="onevsmany">
98 <when value="no"> 82 <param name="controlgroup" argument="--controlgroup" type="text" label="Control group label:" value="0" help="Name of group label to be compared to others"/>
99 </when> 83 </when>
100 </conditional> 84 </conditional>
101 </when> 85 <conditional name="advanced">
102 </conditional>
103 <conditional name="cond">
104 <param name="type_selector" argument="--option" type="select" label="Input format:">
105 <option value="datasets" selected="true">RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N</option>
106 <option value="dataset_class">RNAseq of all samples + sample group specification</option>
107 <option value="datasets_rasonly" selected="true">RNAseq dataset</option>
108 </param>
109 <when value="datasets">
110 <repeat name="input_Datasets" title="RNAseq" min="2">
111 <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
112 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
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 parameters for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps."> 86 <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.">
116 <option value="true" selected="true">No</option> 87 <option value="true" selected="true">No</option>
117 <option value="false">Yes</option> 88 <option value="false">Yes</option>
118 </param> 89 </param>
119 <when value="false"> 90 <when value="false"></when>
91 <when value="true">
92 <conditional name="cond_map">
93 <param name="choice" type="boolean" checked="false" label="Use custom map?" help="Use this option only if you have generated RAS using a custom set of rules">
94 <option value="false" selected="true">No</option>
95 <option value="true">Yes</option>
96 </param>
97 <when value="true">
98 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
99 </when>
100 </conditional>
101 <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />
102 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
103 <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?" />
104 <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?" />
120 </when> 105 </when>
121 <when value="true"> 106 </conditional>
122 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> 107 </when>
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" /> 108 <when value="dataset_class">
124 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" /> 109 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RAS of all samples" />
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?" /> 110 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
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?" /> 111 <conditional name="comparis">
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" /> 112 <param name="comparison" argument="--comparison" type="select" label="Groups comparison:">
113 <option value="manyvsmany" selected="true">One vs One</option>
114 <option value="onevsrest">One vs All</option>
115 <option value="onevsmany">One vs Control</option>
116 </param>
117 <when value="onevsmany">
118 <param name="controlgroup" argument="--controlgroup" type="text" label="Control group label:" value="0" help="Name of group label to be compared to others"/>
128 </when> 119 </when>
129 </conditional> 120 </conditional>
130 </when> 121 <conditional name="advanced">
131 <when value="datasets_rasonly"> 122 <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.">
132 <param name="input_Datasets" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" /> 123 <option value="true" selected="true">No</option>
133 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" /> 124 <option value="false">Yes</option>
134 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> 125 </param>
135 </when> 126 <when value="false"></when>
136 <when value="dataset_class"> 127 <when value="true">
137 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" /> 128 <conditional name="cond_map">
138 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" /> 129 <param name="choice" type="boolean" checked="false" label="Use custom map?" help="Use this option only if you have generated RAS using a custom set of rules">
139 <conditional name="advanced"> 130 <option value="false" selected="true">No</option>
140 <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."> 131 <option value="true">Yes</option>
141 <option value="true" selected="true">No</option> 132 </param>
142 <option value="false">Yes</option> 133 <when value="true">
143 </param> 134 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
144 <when value="false"> 135 </when>
145 </when> 136 </conditional>
146 <when value="true"> 137 <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />
147 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> 138 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
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" /> 139 <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?" />
149 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" /> 140 <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?" />
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?" /> 141 </when>
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?" /> 142 </conditional>
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" /> 143 </when>
153 </when> 144 </conditional>
154 </conditional> 145 </inputs>
155 </when> 146 <outputs>
156 </conditional> 147 <data format="txt" name="log" label="MaREA - Log" />
157 148 <collection name="results" type="list" label="MaREA - Results">
158 149 <discover_datasets pattern="__name_and_ext__" directory="result"/>
159
160
161 </inputs>
162
163 <outputs>
164 <data format="txt" name="log" label="MaREA - Log" />
165 <data format="tabular" name="ras_single" label="MaREA - RAS - ${cond.input_name}">
166 <filter>cond['type_selector'] == "datasets_rasonly"</filter>
167 </data>
168 <collection name="results" type="list" label="MaREA - Results">
169 <filter>cond['type_selector'] == "datasets" or cond['type_selector'] == "dataset_class"</filter>
170 <discover_datasets pattern="__name_and_ext__" directory="result"/>
171 </collection>
172 <collection name="ras" type="list" label="MaREA - RAS list" format_source="tabular">
173 <filter>cond['type_selector'] != "datasets_rasonly" and cond['advanced']['choice'] and cond['advanced']['generateRas']</filter>
174 <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/>
175 </collection> 150 </collection>
176 151 </outputs>
177 </outputs> 152 <help>
178 <tests> 153 <![CDATA[
179 <test>
180 <param name="pValue" value="0.56"/>
181 <output name="log" file="log.txt"/>
182 </test>
183 </tests>
184 <help>
185 <![CDATA[
186 154
187 What it does 155 What it does
188 ------------- 156 -------------
189 157
190 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. 158 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.
266 .. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724 234 .. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
267 .. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj 235 .. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj
268 .. _MaREA cluster analysis: http://link del tool di cluster.org 236 .. _MaREA cluster analysis: http://link del tool di cluster.org
269 237
270 ]]> 238 ]]>
271 </help> 239 </help>
272 <expand macro="citations" /> 240 <expand macro="citations" />undefined</tool>
273 </tool>
274 241