annotate Marea/marea.xml @ 11:d185506631e1 draft

Uploaded
author bimib
date Wed, 13 Feb 2019 05:06:53 -0500
parents 7c76e8e319c2
children 3d77287caf22
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
cf3d3d8f4ef5 Modifica a xml
bimib
parents: 3
diff changeset
1 <tool id="MaREA" name="Metabolic Enrichment Analysis" version="1.0.0">
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
2 <description>for Galaxy</description>
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
3 <macros>
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
4 <import>marea_macros.xml</import>
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
5 </macros>
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
6 <requirements>
5
146cb8e171b8 revision: xml requirement version
bimib
parents: 4
diff changeset
7 <requirement type="package" version="0.23.0">pandas</requirement>
146cb8e171b8 revision: xml requirement version
bimib
parents: 4
diff changeset
8 <requirement type="package" version="1.1.0">scipy</requirement>
6
5721182715a7 xml requirement
bimib
parents: 5
diff changeset
9 <requirement type="package" version="0.10.1">cobra</requirement>
5
146cb8e171b8 revision: xml requirement version
bimib
parents: 4
diff changeset
10 <requirement type="package" version="4.2.1">lxml</requirement>
146cb8e171b8 revision: xml requirement version
bimib
parents: 4
diff changeset
11 <requirement type="package" version="0.8.1">svglib</requirement>
146cb8e171b8 revision: xml requirement version
bimib
parents: 4
diff changeset
12 <requirement type="package" version="3.4.0">reportlab</requirement>
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
13 </requirements>
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
14 <command detect_errors="exit_code">
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
15 <![CDATA[
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
16 python $__tool_directory__/marea.py
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
17 --rules_selector $cond_rule.rules_selector
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
18 #if $cond_rule.rules_selector == 'Custom':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
19 --custom ${cond_rule.Custom_rules}
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
20 --yes_no ${cond_rule.cond_map.yes_no}
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
21 #if $cond_rule.cond_map.yes_no == 'yes':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
22 --custom_map $cond_rule.cond_map.Custom_map
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
23 #end if
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
24 #end if
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
25 --none $None
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
26 --pValue $pValue
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
27 --fChange $fChange
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
28 --tool_dir $__tool_directory__
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
29 --option $cond.type_selector
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
30 --out_log $log
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
31 #if $cond.type_selector == 'datasets':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
32 --input_datas
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
33 #for $data in $cond.input_Datasets:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
34 ${data.input}
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
35 #end for
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
36 --names
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
37 #for $data in $cond.input_Datasets:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
38 ${data.input_name}
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
39 #end for
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
40 #elif $cond.type_selector == 'dataset_class':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
41 --input_data ${input_data}
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
42 --input_class ${input_class}
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
43 #end if
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
44 ]]>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
45 </command>
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
46
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
47 <inputs>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
48 <conditional name="cond_rule">
2
3b3d0e5d0802 Uploaded
bimib
parents: 1
diff changeset
49 <expand macro="options"/>
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
50 <when value="HMRcore">
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
51 </when>
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
52 <when value="Recon">
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
53 </when>
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
54 <when value="Custom">
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
55 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
56 <conditional name="cond_map">
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
57 <param name="yes_no" type="select" label="Custom map? (optional)">
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
58 <option value="no" selected="true">no</option>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
59 <option value="yes">yes</option>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
60 </param>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
61 <when value="yes">
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
62 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
63 </when>
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
64 <when value="no">
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
65 </when>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
66 </conditional>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
67 </when>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
68 </conditional>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
69 <conditional name="cond">
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
70 <param name="type_selector" argument="--option" type="select" label="Input format:">
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
71 <option value="datasets" selected="true">RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N</option>
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
72 <option value="dataset_class">RNAseq of all samples + sample group specification</option>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
73 </param>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
74 <when value="datasets">
4
cf3d3d8f4ef5 Modifica a xml
bimib
parents: 3
diff changeset
75 <repeat name="input_Datasets" title="RNAseq" min="2">
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
76 <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
77 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Defalut: Dataset" />
4
cf3d3d8f4ef5 Modifica a xml
bimib
parents: 3
diff changeset
78 </repeat>
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
79 </when>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
80 <when value="dataset_class">
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
81 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
82 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
83 </when>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
84 </conditional>
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
85 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
9
7c76e8e319c2 fix cluster file and help section
bimib
parents: 6
diff changeset
86 <param name="pValue" argument="--pValue" type="float" size="20" value="0.05" max="1" min="0" label="P-value threshold:" help="min value 0" />
7c76e8e319c2 fix cluster file and help section
bimib
parents: 6
diff changeset
87 <param name="fChange" argument="--fChange" type="float" size="20" value="1.5" min="1" label="Fold-Change threshold:" help="min value 1" />
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
88 </inputs>
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
89
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
90 <outputs>
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
91 <data format="txt" name="log" label="Log" />
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
92 <collection name="map_svg" type="list" label="Graphical results (.svg)">
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
93 <filter>(cond_rule['rules_selector'] == 'HMRcore') or ((cond_rule['rules_selector'] == 'Custom') and (cond_rule['cond_map']['yes_no'] == 'yes'))</filter>
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
94 <discover_datasets pattern="__name_and_ext__" directory="map_svg" />
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
95 </collection>
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
96 <collection name="map_pdf" type="list" label="Graphical results (.pdf)">
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
97 <filter>(cond_rule['rules_selector'] == 'HMRcore') or ((cond_rule['rules_selector'] == 'Custom') and (cond_rule['cond_map']['yes_no'] == 'yes'))</filter>
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
98 <discover_datasets pattern="__name_and_ext__" directory="map_pdf" />
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
99 </collection>
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
100 <collection name="table_out" type="list" label="Tabular results">
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
101 <discover_datasets pattern="__name_and_ext__" directory="table_out" />
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
102 </collection>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
103 </outputs>
4
cf3d3d8f4ef5 Modifica a xml
bimib
parents: 3
diff changeset
104 <tests>
cf3d3d8f4ef5 Modifica a xml
bimib
parents: 3
diff changeset
105 <test>
cf3d3d8f4ef5 Modifica a xml
bimib
parents: 3
diff changeset
106 <param name="pValue" value="0.56"/>
cf3d3d8f4ef5 Modifica a xml
bimib
parents: 3
diff changeset
107 <output name="log" file="log.txt"/>
cf3d3d8f4ef5 Modifica a xml
bimib
parents: 3
diff changeset
108 </test>
cf3d3d8f4ef5 Modifica a xml
bimib
parents: 3
diff changeset
109 </tests>
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
110 <help>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
111 <![CDATA[
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
112
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
113 What it does
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
114 -------------
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
115
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
116 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.
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
117
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
118 Accepted files are:
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
119 - 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*");
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
120 - option 2) one RNA dataset and one class-file specifying the class/condition each sample belongs to.
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
121
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
122 Optional files:
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
123 - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
124
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
125 * (Cobra Toolbox and CobraPy compliant) xml of metabolic model;
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
126 * .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2).
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
127 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
128
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
129 The tool generates:
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
130 1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes;
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
131 2) a metabolic map file (downlodable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
132 3) a log file (.txt).
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
133
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
134 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.
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
135
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
136 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).
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
137
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
138 To calculate P-Values and Fold-Changes and to generate maps, comparisons are performed for each possible pair of classes.
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
139
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
140 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".
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
141
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
142
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
143 Example input
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
144 -------------
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
145
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
146 **"Custom Rules"** option:
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
147
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
148 Custom Rules Dastaset:
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
149
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
150 @CUSTOM_RULES_EXEMPLE@
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
151
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
152 **"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option:
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
153
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
154 RNA-seq Dataset 1:
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
155
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
156 @DATASET_EXEMPLE1@
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
157
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
158 RNA-seq Dataset 2:
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
159
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
160 @DATASET_EXEMPLE2@
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
161
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
162 **"RNAseq of all samples + sample group specification"** option:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
163
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
164 RNA-seq Dataset:
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
165
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
166 @DATASET_EXEMPLE1@
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
167
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
168 Class-file:
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
169
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
170 +------------+------------+
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
171 | Patient_ID | class |
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
172 +============+============+
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
173 | TCGAAA3529 | MSI |
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
174 +------------+------------+
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
175 | TCGAA62671 | MSS |
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
176 +------------+------------+
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
177 | TCGAA62672 | MSI |
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
178 +------------+------------+
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
179
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
180 |
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
181
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
182 .. class:: infomark
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
183
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
184 **TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
185
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
186 .. class:: infomark
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
187
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
188 **TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_.
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
189
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
190 @REFERENCE@
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
191
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
192 .. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
193 .. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
194 .. _MaREA cluster analysis: http://link del tool di cluster.org
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
195
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
196 ]]>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
197 </help>
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
198 <expand macro="citations" />
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
199 </tool>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
200