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comparison all_by_all_correlation.xml @ 1:ec9ee8edb84d draft

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Initial upload of 21.6.10 release.
author malex
date Fri, 18 Jun 2021 20:23:19 +0000
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0:864fc6430432 1:ec9ee8edb84d
1 <tool id="allByAllCorr" name="Metabolite - Gene Correlation" version="@WRAPPER_VERSION@">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 all_by_all_correlation.py
9 -g=$geneDataset
10 -gid=$geneId
11 #if $geneAnnotation.useGeneAnnot == "Yes":
12 -ga=$geneAnnotation.geneAnnot
13 -gn=$geneAnnotation.geneAnnotName
14 #end if
15 -m=$metDataset
16 -mid=$metId
17 #if $metAnnotation.useMetAnnot == "Yes":
18 -ma=$metAnnotation.metAnnot
19 -mn=$metAnnotation.metAnnotName
20 #end if
21 -me=$method
22 -t=$threshold
23 -o=$output
24 -c=$corMat
25 -f=$figure
26 ]]></command>
27 <inputs>
28 <param name="geneDataset" type="data" format="tabular" label="Gene Expression Wide Dataset" help="Select the Gene Expression Wide Dataset from your history"/>
29 <param name="geneId" type="text" size="30" value="" label="Unique Gene FeatureID" help="Name of the Column in your Gene Expression Wide Dataset that contains unique identifiers."/>
30 <conditional name="geneAnnotation">
31 <param name="useGeneAnnot" type="select" label="Use Annotation File?" help="You can chose to input a file containing gene annotation information (e.g. gene names, identifiers, etc.) for labeling output files.">
32 <option value="No">No</option>
33 <option value="Yes">Yes</option>
34 </param>
35 <when value="Yes">
36 <param name="geneAnnot" type="data" format="tabular" label="Gene Expression Annotation File" help="Select the Gene Expression Annotation File from your history"/>
37 <param name="geneAnnotName" type="text" value="" label="Gene Labels" help="Name of the column in the Gene Expression Annotation File to use for labeling output files."/>
38 </when>
39 </conditional>
40 <param name="metDataset" type="data" format="tabular" label="Metabolite Wide Dataset" help="Select the Metabolite Wide Dataset from your history"/>
41 <param name="metId" type="text" size="30" value="" label="Unique Metabolite FeatureID" help="Name of the column in your Metabolite Wide Dataset that contains unique identifiers."/>
42 <conditional name="metAnnotation">
43 <param name="useMetAnnot" type="select" label="Use Annotation File?" help="You can chose to input a file containing metabolite annotation information (e.g. metabolite names, identifiers, etc.) for labeling output files.">
44 <option value="No">No</option>
45 <option value="Yes">Yes</option>
46 </param>
47 <when value="Yes">
48 <param name="metAnnot" type="data" format="tabular" label="Metabolite Annotation File" help="Select the Metabolite Annotation File from your history"/>
49 <param name="metAnnotName" type="text" value="" label="Metabolite Labels" help="Name of the column in the Metabolite Annotation File to use for labeling output files"/>
50 </when>
51 </conditional>
52 <param name="method" type="select" label="Correlation Method" help="Select a correlation method.">
53 <option value="pearson">Pearson</option>
54 <option value="spearman">Spearman</option>
55 <option value="kendall">Kendall</option>
56 </param>
57 <param name="threshold" type="text" value="0.05" label="P-Value threshold." help="Default: 0.05"/>
58 </inputs>
59 <outputs>
60 <data format="tabular" name="output" label="${tool.name} on ${on_string}: Correlation File"/>
61 <data format="tabular" name="corMat" label="${tool.name} on ${on_string}: Correlation Matrix"/>
62 <data format="pdf" name="figure" label="${tool.name} on ${on_string}: Correlation Figure"/>
63 </outputs>
64 <tests>
65 <test>
66 <param name="geneDataset" value="gene_wide_dataset_01fhl.tsv"/>
67 <param name="geneId" value="UniqueID"/>
68 <param name="geneAnnot" value="gene_annotation_file_01fhl.tsv"/>
69 <param name="geneName" value="GeneName"/>
70 <param name="metDataset" value="metabolite_wide_dataset_01fhl.tsv"/>
71 <param name="metId" value="UniqueID"/>
72 <param name="metAnnot" value="metabolite_annotation_file_01fhl.tsv"/>
73 <param name="metName" value="MetName"/>
74 <output name="output" file="correlation_file_01fhl.tsv"/>
75 <output name="corMat" file="correlation_matrix_01fhl.tsv"/>
76 <output name="figure" file="correlation_figure_01fhl.pdf"/>
77 </test>
78 </tests>
79 <help><![CDATA[
80
81 **Tool Description**
82
83 The tool performs a correlation analysis between genes (in a gene expression wide dataset) and metabolites (in a metabolite wide dataset)
84 to generate a table of correlation coefficients. P-values for the correlation coefficients are calculated by simulating individual gene and
85 metabolite datasets 1000 times using a normal distribution with means and standard deviations generated from the data. Sample size reflects
86 the input datasets. Correlations are calculated on the simulated data. Correlations must be higher/lower than 95% of the randomly simulated
87 values to be considered significant.
88
89 --------------------------------------------------------------------------------
90
91 **Input**
92
93 (1) **Gene Expression Dataset** A wide formatted dataset containing measurements for each sample (where samples are in columns):
94
95 +-----------+---------+---------+---------+-----+
96 | UniqueID | sample1 | sample2 | sample3 | ... |
97 +===========+=========+=========+=========+=====+
98 | gene_1 | 1.2 | 3.5 | 2.9 | ... |
99 +-----------+---------+---------+---------+-----+
100 | gene_2 | 1.6 | 3.2 | 3.2 | ... |
101 +-----------+---------+---------+---------+-----+
102 | gene_3 | 1.4 | 3.0 | 3.1 | ... |
103 +-----------+---------+---------+---------+-----+
104 | gene_4 | 1.6 | 2.9 | 3.1 | ... |
105 +-----------+---------+---------+---------+-----+
106 | ... | ... | ... | ... | ... |
107 +-----------+---------+---------+---------+-----+
108
109 (2) **Unique Gene FeatureID** Name of the column in your Gene Expression Wide Dataset that contains unique gene identifiers. **NOTE:** This identifier must be the gene symbol.
110
111 (3) **Metabolomic Wide Dataset** A wide formatted metabolomic dataset that contains measurements for each sample (where samples are in columns):
112
113 +------------+---------+---------+---------+-----+
114 | UniqueID | sample1 | sample2 | sample3 | ... |
115 +============+=========+=========+=========+=====+
116 | met_1 | 10 | 20 | 10 | ... |
117 +------------+---------+---------+---------+-----+
118 | met_2 | 5 | 22 | 30 | ... |
119 +------------+---------+---------+---------+-----+
120 | met_3 | 30 | 27 | 2 | ... |
121 +------------+---------+---------+---------+-----+
122 | met_4 | 32 | 17 | 8 | ... |
123 +------------+---------+---------+---------+-----+
124 | ... | ... | ... | ... | ... |
125 +------------+---------+---------+---------+-----+
126
127 (4) **Unique Metabolite FeatureID** Name of the column in your Metabolite Wide Dataset that contains unique metabolite identifiers.
128
129 (5) **Annotation Files** The user can provide (optional) Annotation Files for the Gene Expression and/or Metabolite Datasets to label the results for easier readability. The user must provide the name of the column with the desired feature name (e.g. Gene Symbol).
130
131 +-----------+------------+-------------+-----+
132 | UniqueID | ENSEMBL_ID | Gene_Symbol | ... |
133 +===========+============+=============+=====+
134 | gene_1 | ENS... | one | ... |
135 +-----------+------------+-------------+-----+
136 | gene_2 | ENS... | two | ... |
137 +-----------+------------+-------------+-----+
138 | gene_3 | ENS... | three | ... |
139 +-----------+------------+-------------+-----+
140 | gene_4 | ENS... | four | ... |
141 +-----------+------------+-------------+-----+
142 | ... | ... | ... | ... |
143 +-----------+------------+-------------+-----+
144
145 (6) **Correlation method** Select the correlation coefficient to be computed from the list. Pearson, kendall, or spearman are available.
146
147 (7) **P-Value threshold** User specified value that limits the data in the resulting 'Correlation File' to only those correlations with P-values less than this value.
148
149 --------------------------------------------------------------------------------
150
151 **Output**
152
153 The user will obtain three outputs from the Gene - Metabolite Correlation Tool:
154
155 (1) **Correlation File.** A file sorted by the absolute values of the correlation coeficient and including the P-value. The file contains only the correlation coefficients where the associated P-values is less than a user-specified value (default = 0.05).
156
157 +--------+------------+-------------+-----------+
158 | Gene | Metabolite | Correlation | (p-value) |
159 +========+============+=============+===========+
160 | gene_1 | met_1 | 0.99 | 0.000 |
161 +--------+------------+-------------+-----------+
162 | gene_2 | met_4 | -0.98 | 0.000 |
163 +--------+------------+-------------+-----------+
164 | gene_3 | met_5 | 0.96 | 0.001 |
165 +--------+------------+-------------+-----------+
166 | gene_4 | met_1 | 0.95 | 0.002 |
167 +--------+------------+-------------+-----------+
168 | ... | ... | ... | ... |
169 +--------+------------+-------------+-----------+
170
171 (2) **Correlation Matrix.** Output correlation matrix.
172
173 +--------+-------+-------+-------+-------+-----+
174 | Gene | met_1 | met_2 | met_3 | met_4 | ... |
175 +========+=======+=======+=======+=======+=====+
176 | gene_1 | 0.99 | 0.56 | 0.25 | 0.33 | ... |
177 +--------+-------+-------+-------+-------+-----+
178 | gene_2 | -0.57 | 0.63 | -0.14 | 0.01 | ... |
179 +--------+-------+-------+-------+-------+-----+
180 | gene_3 | 0.62 | 0.96 | 0.20 | 0.32 | ... |
181 +--------+-------+-------+-------+-------+-----+
182 | gene_4 | 0.95 | 0.25 | 0.16 | 0.44 | ... |
183 +--------+-------+-------+-------+-------+-----+
184 | ... | ... | ... | ... | ... | ... |
185 +--------+-------+-------+-------+-------+-----+
186
187 (3) **Correlation Figure.** Network representation of the top 500 gene-metabolite correlations based on the absolute value of the correlation coeficients. Maximum number of correlations in the netork is 500.
188
189 ]]>
190 </help>
191 <citations>
192 <citation type="bibtex">@article{dejean2013mixomics,
193 title={mixOmics: Omics data integration project},
194 author={Dejean, Sebastien and Gonzalez, Ignacio and L{\^e} Cao, Kim-Anh and Monget, Pierre and Coquery, J and Yao, F and Liquet, B and Rohart, F},
195 journal={R package},
196 year={2013}
197 }</citation>
198 <citation type="bibtex">@ARTICLE{Kirpich17secimtools,
199 author = {Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse, Lauren M. McIntyre},
200 title = {SECIMTools: A suite of Metabolomics Data Analysis Tools},
201 journal = {BMC Bioinformatics},
202 year = {in press}
203 }</citation>
204 <citation type="bibtex">
205 @article{garcia2010paintomics,
206 title={Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data},
207 author={Garc{\'\i}a-Alcalde, Fernando and Garc{\'\i}a-L{\'o}pez, Federico and Dopazo, Joaqu{\'\i}n and Conesa, Ana},
208 journal={Bioinformatics},
209 volume={27},
210 number={1},
211 pages={137--139},
212 year={2010},
213 publisher={Oxford University Press}
214 }</citation>
215 </citations>
216 </tool>