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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
author malex
date Thu, 29 Jul 2021 20:48:10 +0000
parents ec9ee8edb84d
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1:ec9ee8edb84d 2:2c218a253d56
26 ]]></command> 26 ]]></command>
27 <inputs> 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"/> 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."/> 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"> 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."> 31 <param name="useGeneAnnot" type="select" label="Use Annotation File?" help="You can choose to input a file containing gene annotation information (e.g. gene names, identifiers, etc.) for labeling output files.">
32 <option value="No">No</option> 32 <option value="No">No</option>
33 <option value="Yes">Yes</option> 33 <option value="Yes">Yes</option>
34 </param> 34 </param>
35 <when value="Yes"> 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"/> 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."/> 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> 38 </when>
39 <when value="No" />
39 </conditional> 40 </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="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 <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 <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 <param name="useMetAnnot" type="select" label="Use Annotation File?" help="You can choose 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="No">No</option>
45 <option value="Yes">Yes</option> 46 <option value="Yes">Yes</option>
46 </param> 47 </param>
47 <when value="Yes"> 48 <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="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 <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 </when>
52 <when value="No" />
51 </conditional> 53 </conditional>
52 <param name="method" type="select" label="Correlation Method" help="Select a correlation method."> 54 <param name="method" type="select" label="Correlation Method" help="Select a correlation method.">
53 <option value="pearson">Pearson</option> 55 <option value="pearson">Pearson</option>
54 <option value="spearman">Spearman</option> 56 <option value="spearman">Spearman</option>
55 <option value="kendall">Kendall</option> 57 <option value="kendall">Kendall</option>
61 <data format="tabular" name="corMat" label="${tool.name} on ${on_string}: Correlation Matrix"/> 63 <data format="tabular" name="corMat" label="${tool.name} on ${on_string}: Correlation Matrix"/>
62 <data format="pdf" name="figure" label="${tool.name} on ${on_string}: Correlation Figure"/> 64 <data format="pdf" name="figure" label="${tool.name} on ${on_string}: Correlation Figure"/>
63 </outputs> 65 </outputs>
64 <tests> 66 <tests>
65 <test> 67 <test>
66 <param name="geneDataset" value="gene_wide_dataset_01fhl.tsv"/> 68 <param name="geneDataset" value="gene_wide_dataset.tsv"/>
67 <param name="geneId" value="UniqueID"/> 69 <param name="geneId" value="UniqueID"/>
68 <param name="geneAnnot" value="gene_annotation_file_01fhl.tsv"/> 70 <param name="geneAnnot" value="gene_annotation.tsv"/>
69 <param name="geneName" value="GeneName"/> 71 <param name="geneName" value="GeneName"/>
70 <param name="metDataset" value="metabolite_wide_dataset_01fhl.tsv"/> 72 <param name="metDataset" value="metabolite_wide_dataset.tsv"/>
71 <param name="metId" value="UniqueID"/> 73 <param name="metId" value="UniqueID"/>
72 <param name="metAnnot" value="metabolite_annotation_file_01fhl.tsv"/> 74 <param name="metAnnot" value="metabolite_annotation.tsv"/>
73 <param name="metName" value="MetName"/> 75 <param name="metName" value="MetName"/>
74 <output name="output" file="correlation_file_01fhl.tsv"/> 76 <output name="output" file="correlation.tsv" compare="diff" lines_diff="10000"/>
75 <output name="corMat" file="correlation_matrix_01fhl.tsv"/> 77 <output name="corMat" file="correlation_matrix.tsv" compare="diff" lines_diff="10000"/>
76 <output name="figure" file="correlation_figure_01fhl.pdf"/> 78 <output name="figure" file="correlation_figure.pdf" compare="sim_size" delta="1000000"/>
77 </test> 79 </test>
78 </tests> 80 </tests>
79 <help><![CDATA[ 81 <help><![CDATA[
80 82
81 **Tool Description** 83 **Tool Description**
82 84
83 The tool performs a correlation analysis between genes (in a gene expression wide dataset) and metabolites (in a metabolite wide dataset) 85 The tool performs a correlation analysis between genes (Gene Expression Wide Dataset) and
84 to generate a table of correlation coefficients. P-values for the correlation coefficients are calculated by simulating individual gene and 86 metabolites (Metabolite Wide Dataset) to generate
85 metabolite datasets 1000 times using a normal distribution with means and standard deviations generated from the data. Sample size reflects 87 a table of correlation coefficients. P-values for the correlation coefficients are calculated by
86 the input datasets. Correlations are calculated on the simulated data. Correlations must be higher/lower than 95% of the randomly simulated 88 simulating gene and metabolite datasets 1000 times using the mean and standard deviation of both
87 values to be considered significant. 89 datasets.
90
91 The tool outputs 2 TSV files and a PDF figure. The 'correlation file' contains gene-metabolite
92 correlation coefficients with p-values
93 less than the user-specified threshold. The tool also outputs the results in matrix format, the
94 ‘correlation matrix file’. The ‘correlation
95 figure’ is a network representation of the top 500 gene-metabolite correlations based on the
96 absolute value of the correlation coefficients.
88 97
89 -------------------------------------------------------------------------------- 98 --------------------------------------------------------------------------------
90 99
91 **Input** 100 **Input**
92 101
126 135
127 (4) **Unique Metabolite FeatureID** Name of the column in your Metabolite Wide Dataset that contains unique metabolite identifiers. 136 (4) **Unique Metabolite FeatureID** Name of the column in your Metabolite Wide Dataset that contains unique metabolite identifiers.
128 137
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). 138 (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).
130 139
131 +-----------+------------+-------------+-----+ 140 +-----------+--------------+-------------+-----+
132 | UniqueID | ENSEMBL_ID | Gene_Symbol | ... | 141 | UniqueID | ENSEMBL_ID | Gene_Symbol | ... |
133 +===========+============+=============+=====+ 142 +===========+==============+=============+=====+
134 | gene_1 | ENS... | one | ... | 143 | gene_1 | ENS... | one | ... |
135 +-----------+------------+-------------+-----+ 144 +-----------+--------------+-------------+-----+
136 | gene_2 | ENS... | two | ... | 145 | gene_2 | ENS... | two | ... |
137 +-----------+------------+-------------+-----+ 146 +-----------+--------------+-------------+-----+
138 | gene_3 | ENS... | three | ... | 147 | gene_3 | ENS... | three | ... |
139 +-----------+------------+-------------+-----+ 148 +-----------+--------------+-------------+-----+
140 | gene_4 | ENS... | four | ... | 149 | gene_4 | ENS... | four | ... |
141 +-----------+------------+-------------+-----+ 150 +-----------+--------------+-------------+-----+
142 | ... | ... | ... | ... | 151 | ... | ... | ... | ... |
143 +-----------+------------+-------------+-----+ 152 +-----------+--------------+-------------+-----+
144 153
145 (6) **Correlation method** Select the correlation coefficient to be computed from the list. Pearson, kendall, or spearman are available. 154 (6) **Correlation method** Select the correlation coefficient to be computed from the list. Pearson, kendall, or spearman are available.
146 155
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. 156 (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.
148 157
150 159
151 **Output** 160 **Output**
152 161
153 The user will obtain three outputs from the Gene - Metabolite Correlation Tool: 162 The user will obtain three outputs from the Gene - Metabolite Correlation Tool:
154 163
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). 164 (1) **Correlation File.** A file sorted by the absolute values of the correlation coefficient 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).
156 165
157 +--------+------------+-------------+-----------+ 166 +--------+------------+-------------+-----------+
158 | Gene | Metabolite | Correlation | (p-value) | 167 | Gene | Metabolite | Correlation | (p-value) |
159 +========+============+=============+===========+ 168 +========+============+=============+===========+
160 | gene_1 | met_1 | 0.99 | 0.000 | 169 | gene_1 | met_1 | 0.99 | 0.000 |
182 | gene_4 | 0.95 | 0.25 | 0.16 | 0.44 | ... | 191 | gene_4 | 0.95 | 0.25 | 0.16 | 0.44 | ... |
183 +--------+-------+-------+-------+-------+-----+ 192 +--------+-------+-------+-------+-------+-----+
184 | ... | ... | ... | ... | ... | ... | 193 | ... | ... | ... | ... | ... | ... |
185 +--------+-------+-------+-------+-------+-----+ 194 +--------+-------+-------+-------+-------+-----+
186 195
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. 196 (3) **Correlation Figure.** Network representation of the top 500 gene-metabolite correlations based on the absolute value of the correlation coefficients. Maximum number of correlations in the network is 500.
188 197
189 ]]> 198 ]]>
190 </help> 199 </help>
191 <citations> 200 <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, 201 <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}, 202 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}, 203 title = {SECIMTools: A suite of Metabolomics Data Analysis Tools},
201 journal = {BMC Bioinformatics}, 204 journal = {BMC Bioinformatics},
202 year = {in press} 205 year = {2018}
203 }</citation> 206 }</citation>
204 <citation type="bibtex"> 207 <citation type="bibtex">@article{Mor2021GaitGM,
205 @article{garcia2010paintomics, 208 title={GAIT-GM integrative cross-omics analyses reveal cholinergic defects in a C. elegans model of Parkinson's disease},
206 title={Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data}, 209 author={Mor, DE and Huertas, F and Morse, AM and Kaletsky, R and Murphy, CT and Kalia, V and Miller, GW and Moskalenko, O and Conesa, A and McIntyre, LM},
207 author={Garc{\'\i}a-Alcalde, Fernando and Garc{\'\i}a-L{\'o}pez, Federico and Dopazo, Joaqu{\'\i}n and Conesa, Ana}, 210 journal={BMC Genomics},
208 journal={Bioinformatics}, 211 year={submitted},
209 volume={27},
210 number={1},
211 pages={137--139},
212 year={2010},
213 publisher={Oxford University Press}
214 }</citation> 212 }</citation>
215 </citations> 213 </citations>
216 </tool> 214 </tool>