annotate Marea/marea.xml @ 28:e6831924df01 draft

small fixes (elbow plot and output managment)
author bimib
date Mon, 14 Oct 2019 05:01:08 -0400
parents 100c116d0d25
children 9fcb0e8d6d47
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
26
100c116d0d25 Uploaded
bimib
parents: 16
diff changeset
1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.1">
100c116d0d25 Uploaded
bimib
parents: 16
diff changeset
2 <description></description>
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
3 <macros>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
4 <import>marea_macros.xml</import>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
5 </macros>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
6 <requirements>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
7 <requirement type="package" version="0.23.0">pandas</requirement>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
8 <requirement type="package" version="1.1.0">scipy</requirement>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
9 <requirement type="package" version="0.10.1">cobra</requirement>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
10 <requirement type="package" version="4.2.1">lxml</requirement>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
11 <requirement type="package" version="0.8.1">svglib</requirement>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
12 <requirement type="package" version="3.4.0">reportlab</requirement>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
13 </requirements>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
14 <command detect_errors="exit_code">
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
15 <![CDATA[
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
16 python $__tool_directory__/marea.py
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
17 --rules_selector $cond_rule.rules_selector
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
18 #if $cond_rule.rules_selector == 'Custom':
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
19 --custom ${cond_rule.Custom_rules}
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
20 --yes_no ${cond_rule.cond_map.yes_no}
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
21 #if $cond_rule.cond_map.yes_no == 'yes':
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
22 --custom_map $cond_rule.cond_map.Custom_map
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
23 #end if
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
24 #end if
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
25 #if $advanced.choice == 'true':
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
26 --none ${advanced.None}
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
27 --pValue ${advanced.pValue}
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
28 --fChange ${advanced.fChange}
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
29 --generate_svg ${advanced.generateSvg}
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
30 --generate_pdf ${advanced.generatePdf}
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
31 --generate_ras ${advanced.generateRas}
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
32 #else
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
33 --none true
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
34 --pValue 0.05
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
35 --fChange 1.5
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
36 --generate_svg false
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
37 --generate_pdf true
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
38 --generate_ras false
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
39 #end if
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
40 --tool_dir $__tool_directory__
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
41 --option $cond.type_selector
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
42 --out_log $log
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
43
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
44 #if $cond.type_selector == 'datasets':
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
45 --input_datas
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
46 #for $data in $cond.input_Datasets:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
47 ${data.input}
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
48 #end for
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
49 --names
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
50 #for $data in $cond.input_Datasets:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
51 ${data.input_name}
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
52 #end for
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
53 #elif $cond.type_selector == 'dataset_class':
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
54 --input_data ${input_data}
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
55 --input_class ${input_class}
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
56 #end if
28
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 26
diff changeset
57 #if $cond.type_selector == 'datasets_rasonly':
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 26
diff changeset
58 --input_datas ${input_Datasets}
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 26
diff changeset
59 --single_ras_file $ras_single
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 26
diff changeset
60 #end if
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
61 ]]>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
62 </command>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
63
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
64 <inputs>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
65 <conditional name="cond_rule">
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
66 <expand macro="options"/>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
67 <when value="HMRcore">
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
68 </when>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
69 <when value="Recon">
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
70 </when>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
71 <when value="Custom">
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
72 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
73 <conditional name="cond_map">
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
74 <param name="yes_no" type="select" label="Custom map? (optional)">
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
75 <option value="no" selected="true">no</option>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
76 <option value="yes">yes</option>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
77 </param>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
78 <when value="yes">
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
79 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
80 </when>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
81 <when value="no">
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
82 </when>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
83 </conditional>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
84 </when>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
85 </conditional>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
86 <conditional name="cond">
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
87 <param name="type_selector" argument="--option" type="select" label="Input format:">
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
88 <option value="datasets" selected="true">RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N</option>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
89 <option value="dataset_class">RNAseq of all samples + sample group specification</option>
28
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 26
diff changeset
90 <option value="datasets_rasonly" selected="true">RNAseq dataset</option>
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
91 </param>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
92 <when value="datasets">
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
93 <repeat name="input_Datasets" title="RNAseq" min="2">
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
94 <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
95 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
96 </repeat>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
97 </when>
28
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 26
diff changeset
98 <when value="datasets_rasonly">
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 26
diff changeset
99 <param name="input_Datasets" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 26
diff changeset
100 </when>
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
101 <when value="dataset_class">
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
102 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
103 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
104 </when>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
105 </conditional>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
106
28
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 26
diff changeset
107
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 26
diff changeset
108 <!--TODO: NASCONDERE ADVANCED SE RAS ONLY-->
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 26
diff changeset
109
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
110 <conditional name="advanced">
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
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.">
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
112 <option value="true" selected="true">No</option>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
113 <option value="false">Yes</option>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
114 </param>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
115 <when value="false">
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
116 </when>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
117 <when value="true">
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
118 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
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" />
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
120 <param name="fChange" argument="--fChange" type="float" size="20" value="1.5" min="1" label="Fold-Change threshold:" help="min value 1" />
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
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?" />
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
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?" />
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
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" />
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
124 </when>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
125 </conditional>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
126 </inputs>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
127
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
128 <outputs>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
129 <data format="txt" name="log" label="${tool.name} - Log" />
28
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 26
diff changeset
130 <data format="tabular" name="ras_single" label="${tool.name} - RAS">
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 26
diff changeset
131 <filter>cond['type_selector'] == "datasets_rasonly"</filter>
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 26
diff changeset
132 </data>
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
133 <collection name="results" type="list" label="${tool.name} - Results">
28
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 26
diff changeset
134 <filter>cond['type_selector'] == "datasets" or cond['type_selector'] == "dataset_class"</filter>
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
135 <discover_datasets pattern="__name_and_ext__" directory="result"/>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
136 </collection>
28
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 26
diff changeset
137 <collection name="ras" type="list" label="${tool.name} - RAS list" format_source="tabular">
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
138 <filter>advanced['choice'] and advanced['generateRas']</filter>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
139 <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
140 </collection>
28
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 26
diff changeset
141
16
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
142 </outputs>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
143 <tests>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
144 <test>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
145 <param name="pValue" value="0.56"/>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
146 <output name="log" file="log.txt"/>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
147 </test>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
148 </tests>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
149 <help>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
150 <![CDATA[
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
151
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
152 What it does
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
153 -------------
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
154
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
155 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.
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
156
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
157 Accepted files are:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
158 - 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*");
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
159 - option 2) one RNA dataset and one class-file specifying the class/condition each sample belongs to.
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
160
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
161 Optional files:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
162 - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
163
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
164 * (Cobra Toolbox and CobraPy compliant) xml of metabolic model;
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
165 * .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2).
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
166 - 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
167
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
168 The tool generates:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
169 1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes;
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
170 2) a metabolic map file (downlodable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
171 3) a log file (.txt).
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
172
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
173 RNA-seq datasets format: tab-separated text files, reporting the expression level (e.g., TPM, RPKM, ...) of each gene (row) for a given sample (column). Header: sample ID.
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
174
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
175 Class-file format: each row of the class-file reports the sample ID (column1) and the label of the class/condition the sample belongs to (column 2).
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
176
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
177 To calculate P-Values and Fold-Changes and to generate maps, comparisons are performed for each possible pair of classes.
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
178
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
179 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
180
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
181
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
182 Example input
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
183 -------------
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
184
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
185 **"Custom Rules"** option:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
186
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
187 Custom Rules Dastaset:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
188
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
189 @CUSTOM_RULES_EXEMPLE@
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
190
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
191 **"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
192
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
193 RNA-seq Dataset 1:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
194
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
195 @DATASET_EXEMPLE1@
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
196
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
197 RNA-seq Dataset 2:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
198
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
199 @DATASET_EXEMPLE2@
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
200
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
201 **"RNAseq of all samples + sample group specification"** option:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
202
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
203 RNA-seq Dataset:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
204
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
205 @DATASET_EXEMPLE1@
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
206
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
207 Class-file:
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
208
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
209 +------------+------------+
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
210 | Patient_ID | class |
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
211 +============+============+
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
212 | TCGAAA3529 | MSI |
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
213 +------------+------------+
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
214 | TCGAA62671 | MSS |
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
215 +------------+------------+
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
216 | TCGAA62672 | MSI |
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
217 +------------+------------+
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
218
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
219 |
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
220
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
221 .. class:: infomark
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
222
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
223 **TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
224
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
225 .. class:: infomark
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
226
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
227 **TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_.
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
228
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
229 @REFERENCE@
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
230
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
231 .. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
232 .. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
233 .. _MaREA cluster analysis: http://link del tool di cluster.org
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
234
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
235 ]]>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
236 </help>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
237 <expand macro="citations" />
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
238 </tool>
c71ac0bb12de Uploaded
bimib
parents: 13
diff changeset
239