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author bimib
date Wed, 22 Jan 2020 11:45:41 -0500
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1 <tool id="MaREA RAS Generator" name="RAS Generator" version="1.0.0">
2 <description></description>
3 <macros>
4 <import>marea_macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="0.23.0">pandas</requirement>
8 <requirement type="package" version="1.1.0">scipy</requirement>
9 <requirement type="package" version="0.10.1">cobra</requirement>
10 <requirement type="package" version="4.2.1">lxml</requirement>
11 <requirement type="package" version="0.8.1">svglib</requirement>
12 <requirement type="package" version="3.4.0">reportlab</requirement>
13 </requirements>
14 <command detect_errors="exit_code">
15 <![CDATA[
16 python $__tool_directory__/marea.py
17 --rules_selector $cond_rule.rules_selector
18 --tool_dir $__tool_directory__
19 --option $cond.type_selector
20 --out_log $log
21 --input_datas ${input_Datasets}
22 --single_ras_file $ras_single
23 --none ${cond.None}
24 #end if
25 ]]>
26 </command>
27
28 <inputs>
29 <conditional name="cond_rule">
30 <expand macro="options"/>
31 <when value="HMRcore">
32 </when>
33 <when value="Recon">
34 </when>
35 <when value="Custom">
36 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
37 <conditional name="cond_map">
38 <param name="yes_no" type="select" label="Custom map? (optional)">
39 <option value="no" selected="true">no</option>
40 <option value="yes">yes</option>
41 </param>
42 <when value="yes">
43 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
44 </when>
45 <when value="no">
46 </when>
47 </conditional>
48 </when>
49 </conditional>
50 <conditional name="cond">
51
52 <param name="input_Datasets" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
53 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
54 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
55
56
57 </when>
58 </conditional>
59 </inputs>
60
61 <outputs>
62 <data format="txt" name="log" label="MaREA - Log" />
63 <data format="tabular" name="ras_single" label="MaREA - RAS - ${cond.input_name}">
64 <filter>cond['type_selector'] == "datasets_rasonly"</filter>
65 </data>
66 <collection name="results" type="list" label="MaREA - Results">
67 <filter>cond['type_selector'] == "datasets" or cond['type_selector'] == "dataset_class"</filter>
68 <discover_datasets pattern="__name_and_ext__" directory="result"/>
69 </collection>
70 <collection name="ras" type="list" label="MaREA - RAS list" format_source="tabular">
71 <filter>cond['type_selector'] != "datasets_rasonly" and cond['advanced']['choice'] and cond['advanced']['generateRas']</filter>
72 <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/>
73 </collection>
74
75 </outputs>
76 <tests>
77 <test>
78 <param name="pValue" value="0.56"/>
79 <output name="log" file="log.txt"/>
80 </test>
81 </tests>
82 <help>
83 <![CDATA[
84
85 What it does
86 -------------
87
88 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.
89
90 Accepted files are:
91 - 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*");
92 - option 2) one RNA dataset and one class-file specifying the class/condition each sample belongs to.
93
94 Optional files:
95 - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
96
97 * (Cobra Toolbox and CobraPy compliant) xml of metabolic model;
98 * .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2).
99 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
100
101 The tool generates:
102 1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes;
103 2) a metabolic map file (downlodable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
104 3) a log file (.txt).
105
106 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.
107
108 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).
109
110 To calculate P-Values and Fold-Changes and to generate maps, comparisons are performed for each possible pair of classes.
111
112 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".
113
114
115 Example input
116 -------------
117
118 **"Custom Rules"** option:
119
120 Custom Rules Dastaset:
121
122 @CUSTOM_RULES_EXEMPLE@
123
124 **"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option:
125
126 RNA-seq Dataset 1:
127
128 @DATASET_EXEMPLE1@
129
130 RNA-seq Dataset 2:
131
132 @DATASET_EXEMPLE2@
133
134 **"RNAseq of all samples + sample group specification"** option:
135
136 RNA-seq Dataset:
137
138 @DATASET_EXEMPLE1@
139
140 Class-file:
141
142 +------------+------------+
143 | Patient_ID | class |
144 +============+============+
145 | TCGAAA3529 | MSI |
146 +------------+------------+
147 | TCGAA62671 | MSS |
148 +------------+------------+
149 | TCGAA62672 | MSI |
150 +------------+------------+
151
152 |
153
154 .. class:: infomark
155
156 **TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
157
158 .. class:: infomark
159
160 **TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_.
161
162 @REFERENCE@
163
164 .. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
165 .. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj
166 .. _MaREA cluster analysis: http://link del tool di cluster.org
167
168 ]]>
169 </help>
170 <expand macro="citations" />
171 </tool>
172