annotate Marea/marea.xml @ 70:c22ba0547370 draft

update links and pubblications.
author bimib
date Wed, 03 Jun 2020 10:19:48 -0400
parents aa09186cbc9f
children ec499aee95c7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
68
aa09186cbc9f Uploaded
bimib
parents: 67
diff changeset
1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.1.7">
47
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
2 <macros>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
3 <import>marea_macros.xml</import>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
4 </macros>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
5 <requirements>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
6 <requirement type="package" version="0.23.0">pandas</requirement>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
7 <requirement type="package" version="1.1.0">scipy</requirement>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
8 <requirement type="package" version="0.10.1">cobra</requirement>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
9 <requirement type="package" version="4.2.1">lxml</requirement>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
10 <requirement type="package" version="0.8.1">svglib</requirement>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
11 <requirement type="package" version="3.4.0">reportlab</requirement>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
12 </requirements>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
13 <command detect_errors="exit_code">
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
14 <![CDATA[
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
15 python $__tool_directory__/marea.py
47
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
16
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
17 --tool_dir $__tool_directory__
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
18 --option $cond.type_selector
33
abf0bfe01c78 Uploaded
bimib
parents: 32
diff changeset
19 --out_log $log
abf0bfe01c78 Uploaded
bimib
parents: 32
diff changeset
20
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
21 #if $cond.type_selector == 'datasets':
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
22 --input_datas
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
23 #for $data in $cond.input_Datasets:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
24 ${data.input}
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
25 #end for
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
26 --names
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
27 #for $data in $cond.input_Datasets:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
28 ${data.input_name}
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
29 #end for
47
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
30 --comparison ${cond.comparis.comparison}
66
858500ec9767 Uploaded
bimib
parents: 63
diff changeset
31 #if $cond.comparis.comparison == 'onevsmany'
858500ec9767 Uploaded
bimib
parents: 63
diff changeset
32 --control '${cond.comparis.controlgroup}'
63
b8cbc2122d55 Uploaded
bimib
parents: 62
diff changeset
33 #end if
66
858500ec9767 Uploaded
bimib
parents: 63
diff changeset
34
31
944e15aa970a Uploaded
bimib
parents: 29
diff changeset
35 #if $cond.advanced.choice == 'true':
66
858500ec9767 Uploaded
bimib
parents: 63
diff changeset
36 #if $cond.advanced.cond_map.cond_map_choice == 'true':
858500ec9767 Uploaded
bimib
parents: 63
diff changeset
37 --custom_rules true
858500ec9767 Uploaded
bimib
parents: 63
diff changeset
38 --custom_map ${cond.advanced.cond_map.custom_map}
858500ec9767 Uploaded
bimib
parents: 63
diff changeset
39 #end if
47
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
40 --pValue ${cond.advanced.pValue}
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
41 --fChange ${cond.advanced.fChange}
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
42 --generate_svg ${cond.advanced.generateSvg}
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
43 --generate_pdf ${cond.advanced.generatePdf}
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
44 #else
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
45 --pValue 0.05
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
46 --fChange 1.5
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
47 --generate_svg false
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
48 --generate_pdf true
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
49 #end if
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
50 #elif $cond.type_selector == 'dataset_class':
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
51 --input_data ${input_data}
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
52 --input_class ${input_class}
47
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
53 --comparison ${cond.comparis.comparison}
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
54 #if $cond.comparis.comparison == 'onevsmany'
66
858500ec9767 Uploaded
bimib
parents: 63
diff changeset
55 --control '${cond.comparis.controlgroup}'
63
b8cbc2122d55 Uploaded
bimib
parents: 62
diff changeset
56 #end if
31
944e15aa970a Uploaded
bimib
parents: 29
diff changeset
57 #if $cond.advanced.choice == 'true':
66
858500ec9767 Uploaded
bimib
parents: 63
diff changeset
58 #if $cond.advanced.cond_map.cond_map_choice == 'true':
858500ec9767 Uploaded
bimib
parents: 63
diff changeset
59 --custom_rules true
858500ec9767 Uploaded
bimib
parents: 63
diff changeset
60 --custom_map ${cond.advanced.cond_map.custom_map}
858500ec9767 Uploaded
bimib
parents: 63
diff changeset
61 #end if
47
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
62 --pValue ${cond.advanced.pValue}
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
63 --fChange ${cond.advanced.fChange}
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
64 --generate_svg ${cond.advanced.generateSvg}
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
65 --generate_pdf ${cond.advanced.generatePdf}
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
66 #else
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
67 --pValue 0.05
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
68 --fChange 1.5
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
69 --generate_svg false
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
70 --generate_pdf true
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
71 #end if
28
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 26
diff changeset
72 #end if
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
73 ]]>
47
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
74 </command>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
75 <inputs>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
76 <conditional name="cond">
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
77 <param name="type_selector" argument="--option" type="select" label="Input format:">
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
78 <option value="datasets" selected="true">RAS of group 1 + RAS of group 2 + ... + RAS of group N</option>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
79 <option value="dataset_class">RAS of all samples + sample group specification</option>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
80 </param>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
81 <when value="datasets">
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
82 <repeat name="input_Datasets" title="RAS dataset" min="2">
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
83 <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
84 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
85 </repeat>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
86 <conditional name="comparis">
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
87 <param name="comparison" argument="--comparison" type="select" label="Groups comparison:">
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
88 <option value="manyvsmany" selected="true">One vs One</option>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
89 <option value="onevsrest">One vs All</option>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
90 <option value="onevsmany">One vs Control</option>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
91 </param>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
92 <when value="onevsmany">
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
93 <param name="controlgroup" argument="--controlgroup" type="text" label="Control group label:" value="0" help="Name of group label to be compared to others"/>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
94 </when>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
95 </conditional>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
96 <conditional name="advanced">
33
abf0bfe01c78 Uploaded
bimib
parents: 32
diff changeset
97 <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.">
47
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
98 <option value="true" selected="true">No</option>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
99 <option value="false">Yes</option>
31
944e15aa970a Uploaded
bimib
parents: 29
diff changeset
100 </param>
47
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
101 <when value="false"></when>
31
944e15aa970a Uploaded
bimib
parents: 29
diff changeset
102 <when value="true">
47
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
103 <conditional name="cond_map">
66
858500ec9767 Uploaded
bimib
parents: 63
diff changeset
104 <param name="cond_map_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">
47
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
105 <option value="false" selected="true">No</option>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
106 <option value="true">Yes</option>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
107 </param>
66
858500ec9767 Uploaded
bimib
parents: 63
diff changeset
108 <when value="true">
67
3dfffeac4e57 Uploaded
bimib
parents: 66
diff changeset
109 <param name="custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
47
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
110 </when>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
111 </conditional>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
112 <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
113 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
114 <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?" />
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
115 <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?" />
31
944e15aa970a Uploaded
bimib
parents: 29
diff changeset
116 </when>
47
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
117 </conditional>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
118 </when>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
119 <when value="dataset_class">
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
120 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RAS of all samples" />
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
121 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
47
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
122 <conditional name="comparis">
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
123 <param name="comparison" argument="--comparison" type="select" label="Groups comparison:">
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
124 <option value="manyvsmany" selected="true">One vs One</option>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
125 <option value="onevsrest">One vs All</option>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
126 <option value="onevsmany">One vs Control</option>
31
944e15aa970a Uploaded
bimib
parents: 29
diff changeset
127 </param>
47
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
128 <when value="onevsmany">
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
129 <param name="controlgroup" argument="--controlgroup" type="text" label="Control group label:" value="0" help="Name of group label to be compared to others"/>
31
944e15aa970a Uploaded
bimib
parents: 29
diff changeset
130 </when>
47
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
131 </conditional>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
132 <conditional name="advanced">
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
133 <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.">
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
134 <option value="true" selected="true">No</option>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
135 <option value="false">Yes</option>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
136 </param>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
137 <when value="false"></when>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
138 <when value="true">
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
139 <conditional name="cond_map">
66
858500ec9767 Uploaded
bimib
parents: 63
diff changeset
140 <param name="cond_map_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">
47
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
141 <option value="false" selected="true">No</option>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
142 <option value="true">Yes</option>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
143 </param>
66
858500ec9767 Uploaded
bimib
parents: 63
diff changeset
144 <when value="true">
858500ec9767 Uploaded
bimib
parents: 63
diff changeset
145 <param name="custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
47
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
146 </when>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
147 </conditional>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
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" />
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
149 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
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?" />
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
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?" />
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
152 </when>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
153 </conditional>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
154 </when>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
155 </conditional>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
156 </inputs>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
157 <outputs>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
158 <data format="txt" name="log" label="MaREA - Log" />
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
159 <collection name="results" type="list" label="MaREA - Results">
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
160 <discover_datasets pattern="__name_and_ext__" directory="result"/>
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
161 </collection>
47
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
162 </outputs>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
163 <help>
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
164 <![CDATA[
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
165
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
166 What it does
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
167 -------------
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
168
48
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
169 This tool analyzes and visualizes differences in the Reaction Activity Scores (RASs) of groups of samples, as computed by the Expression2RAS tool, of groups of samples.
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
170
33
abf0bfe01c78 Uploaded
bimib
parents: 32
diff changeset
171 Accepted files are:
48
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
172 - option 1) two or more RAS datasets, each referring to samples in a given group. The user can specify a label for each group (as e.g. "classA" and "classB");
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
173 - option 2) one RAS dataset and one group-file specifying the group each sample belongs to.
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
174
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
175 RAS datasets format: tab-separated text files, reporting the RAS value of each reaction (row) for a given sample (column).
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
176
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
177 Column header: sample ID.
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
178 Raw header: reaction ID.
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
179
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
180 Optional files:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
181 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
182
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
183 The tool generates:
48
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
184 - 1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes;
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
185 - 2) a metabolic map file (downloadable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
186 - 3) a log file (.txt).
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
187
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
188 Output options:
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
189 To calculate P-Values and Fold-Changes and to enrich maps, comparisons are performed for each possible pair of groups (default option ‘One vs One’).
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
190
48
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
191 Alternative options are:
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
192 - comparison of each group vs. the rest of samples (option ‘One vs Rest’)
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
193 - comparison of each group vs. a control group (option ‘One vs Control). If this option is selected the user must indicate the control group label.
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
194
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
195 Output files will be named as classA_vs_classB. Reactions will conventionally be reported as up-regulated (down-regulated) if they are significantly more (less) active in class having label "classA".
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
196
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
197 Example input
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
198 -------------
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
199
48
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
200 "RAS of group 1 + RAS of group 2 + ... + RAS of group N" option:
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
201
48
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
202 RAS Dataset 1:
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
203
48
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
204 +------------+----------------+----------------+----------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
205 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
206 +============+================+================+================+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
207 | r1642 | 0.523167 | 0.371355 | 0.925661 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
208 +------------+----------------+----------------+----------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
209 | r1643 | 0.568765 | 0.765567 | 0.456789 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
210 +------------+----------------+----------------+----------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
211 | r1640 | 0.876545 | 0.768933 | 0.987654 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
212 +------------+----------------+----------------+----------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
213 | r1641 | 0.456788 | 0.876543 | 0.876542 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
214 +------------+----------------+----------------+----------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
215 | r1646 | 0.876543 | 0.786543 | 0.897654 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
216 +------------+----------------+----------------+----------------+
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
217
48
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
218 RAS Dataset 2:
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
219
48
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
220 +------------+----------------+----------------+----------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
221 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
222 +============+================+================+================+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
223 | r1642 | 0.523167 | 0.371355 | 0.925661 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
224 +------------+----------------+----------------+----------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
225 | r1643 | 0.568765 | 0.765567 | 0.456789 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
226 +------------+----------------+----------------+----------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
227 | r1640 | 0.876545 | 0.768933 | 0.987654 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
228 +------------+----------------+----------------+----------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
229 | r1641 | 0.456788 | 0.876543 | 0.876542 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
230 +------------+----------------+----------------+----------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
231 | r1646 | 0.876543 | 0.786543 | 0.897654 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
232 +------------+----------------+----------------+----------------+
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
233
48
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
234 "RAS of all samples + sample group specification" option:
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
235
48
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
236 RAS Dataset:
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
237
48
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
238 +------------+----------------+----------------+----------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
239 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
240 +============+================+================+================+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
241 | r1642 | 0.523167 | 0.371355 | 0.925661 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
242 +------------+----------------+----------------+----------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
243 | r1643 | 0.568765 | 0.765567 | 0.456789 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
244 +------------+----------------+----------------+----------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
245 | r1640 | 0.876545 | 0.768933 | 0.987654 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
246 +------------+----------------+----------------+----------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
247 | r1641 | 0.456788 | 0.876543 | 0.876542 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
248 +------------+----------------+----------------+----------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
249 | r1646 | 0.876543 | 0.786543 | 0.897654 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
250 +------------+----------------+----------------+----------------+
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
251
48
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
252 Group-file
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
253
48
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
254 +---------------+-----------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
255 | Patient ID | Class |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
256 +===============+===========+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
257 | TCGAAA3529 | MSI |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
258 +---------------+-----------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
259 | TCGAA62671 | MSS |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
260 +---------------+-----------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
261 | TCGAA62672 | MSI |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
262 +---------------+-----------+
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
263
48
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
264 Advanced options
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
265 ----------------
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
266
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
267 P-Value threshold: the threshold used for significance Kolmogorov-Smirnov (KS) test, to verify whether the distributions of RASs over the samples in two sets are significantly different
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
268
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
269 Fold-Change threshold: threshold of the fold-change between the average RAS of two groups. Among the reactions that pass the KS test, only fold-change values larger than the indicated threshold will be visualized on the output metabolic map;
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
270
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
271
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
272 .. class:: infomark
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
273
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
274 **TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
275
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
276 .. class:: infomark
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
277
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
278 **TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_.
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
279
70
c22ba0547370 update links and pubblications.
bimib
parents: 68
diff changeset
280 .. class:: infomark
c22ba0547370 update links and pubblications.
bimib
parents: 68
diff changeset
281
c22ba0547370 update links and pubblications.
bimib
parents: 68
diff changeset
282 **TIP**: This tool using the RAS scores computed by `Ras tool`_.
c22ba0547370 update links and pubblications.
bimib
parents: 68
diff changeset
283
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
284 @REFERENCE@
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
285
70
c22ba0547370 update links and pubblications.
bimib
parents: 68
diff changeset
286 .. _Ras tool: http://bimib.disco.unimib.it:5555/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbimib%2Fmarea%2FMaREA+RAS+Generator%2F1.0.6&version=1.0.6&__identifer=auulv6gbp76
c22ba0547370 update links and pubblications.
bimib
parents: 68
diff changeset
287 .. _Convert delimiters to TAB: http://bimib.disco.unimib.it:5555/?tool_id=Convert+characters1&version=1.0.0&__identifer=76g7trea4j6
c22ba0547370 update links and pubblications.
bimib
parents: 68
diff changeset
288 .. _MaREA cluster analysis: http://bimib.disco.unimib.it:5555/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbimib%2Fmarea%2FMaREA_cluester%2F1.1.2&version=1.1.2&__identifer=lxbyzn2me9
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
289
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
290 ]]>
47
3af9d394367c Uploaded
bimib
parents: 35
diff changeset
291 </help>
70
c22ba0547370 update links and pubblications.
bimib
parents: 68
diff changeset
292 <expand macro="citations" />
c22ba0547370 update links and pubblications.
bimib
parents: 68
diff changeset
293 </tool>
33
abf0bfe01c78 Uploaded
bimib
parents: 32
diff changeset
294