Mercurial > repos > malex > gait_gm

annotate all_by_all_correlation.xml @ 2:2c218a253d56 draft default tip

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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
children
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1 <tool id="allByAllCorr" name="Metabolite - Gene Correlation" version="@WRAPPER_VERSION@">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 all_by_all_correlation.py
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9 -g=$geneDataset
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10 -gid=$geneId
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11 #if $geneAnnotation.useGeneAnnot == "Yes":
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12 -ga=$geneAnnotation.geneAnnot
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13 -gn=$geneAnnotation.geneAnnotName
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14 #end if
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15 -m=$metDataset
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16 -mid=$metId
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17 #if $metAnnotation.useMetAnnot == "Yes":
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18 -ma=$metAnnotation.metAnnot
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19 -mn=$metAnnotation.metAnnotName
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20 #end if
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21 -me=$method
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22 -t=$threshold
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23 -o=$output
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24 -c=$corMat
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25 -f=$figure
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26 ]]></command>
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27 <inputs>
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28 <param name="geneDataset" type="data" format="tabular" label="Gene Expression Wide Dataset" help="Select the Gene Expression Wide Dataset from your history"/>
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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."/>
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30 <conditional name="geneAnnotation">
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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.">
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32 <option value="No">No</option>
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33 <option value="Yes">Yes</option>
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34 </param>
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35 <when value="Yes">
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36 <param name="geneAnnot" type="data" format="tabular" label="Gene Expression Annotation File" help="Select the Gene Expression Annotation File from your history"/>
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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."/>
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38 </when>
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39 <when value="No" />
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40 </conditional>
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41 <param name="metDataset" type="data" format="tabular" label="Metabolite Wide Dataset" help="Select the Metabolite Wide Dataset from your history"/>
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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."/>
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43 <conditional name="metAnnotation">
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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.">
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45 <option value="No">No</option>
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46 <option value="Yes">Yes</option>
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47 </param>
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48 <when value="Yes">
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49 <param name="metAnnot" type="data" format="tabular" label="Metabolite Annotation File" help="Select the Metabolite Annotation File from your history"/>
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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"/>
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51 </when>
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52 <when value="No" />
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53 </conditional>
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54 <param name="method" type="select" label="Correlation Method" help="Select a correlation method.">
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55 <option value="pearson">Pearson</option>
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56 <option value="spearman">Spearman</option>
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57 <option value="kendall">Kendall</option>
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58 </param>
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59 <param name="threshold" type="text" value="0.05" label="P-Value threshold." help="Default: 0.05"/>
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60 </inputs>
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61 <outputs>
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62 <data format="tabular" name="output" label="${tool.name} on ${on_string}: Correlation File"/>
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63 <data format="tabular" name="corMat" label="${tool.name} on ${on_string}: Correlation Matrix"/>
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64 <data format="pdf" name="figure" label="${tool.name} on ${on_string}: Correlation Figure"/>
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65 </outputs>
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66 <tests>
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67 <test>
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68 <param name="geneDataset" value="gene_wide_dataset.tsv"/>
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69 <param name="geneId" value="UniqueID"/>
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70 <param name="geneAnnot" value="gene_annotation.tsv"/>
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71 <param name="geneName" value="GeneName"/>
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72 <param name="metDataset" value="metabolite_wide_dataset.tsv"/>
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73 <param name="metId" value="UniqueID"/>
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74 <param name="metAnnot" value="metabolite_annotation.tsv"/>
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75 <param name="metName" value="MetName"/>
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76 <output name="output" file="correlation.tsv" compare="diff" lines_diff="10000"/>
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77 <output name="corMat" file="correlation_matrix.tsv" compare="diff" lines_diff="10000"/>
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78 <output name="figure" file="correlation_figure.pdf" compare="sim_size" delta="1000000"/>
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79 </test>
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80 </tests>
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81 <help><![CDATA[
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82
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83 **Tool Description**
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84
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85 The tool performs a correlation analysis between genes (Gene Expression Wide Dataset) and
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86 metabolites (Metabolite Wide Dataset) to generate
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87 a table of correlation coefficients. P-values for the correlation coefficients are calculated by
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88 simulating gene and metabolite datasets 1000 times using the mean and standard deviation of both
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89 datasets.
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90
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91 The tool outputs 2 TSV files and a PDF figure. The 'correlation file' contains gene-metabolite
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92 correlation coefficients with p-values
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93 less than the user-specified threshold. The tool also outputs the results in matrix format, the
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94 ‘correlation matrix file’. The ‘correlation
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95 figure’ is a network representation of the top 500 gene-metabolite correlations based on the
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96 absolute value of the correlation coefficients.
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97
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98 --------------------------------------------------------------------------------
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99
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100 **Input**
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101
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102 (1) **Gene Expression Dataset** A wide formatted dataset containing measurements for each sample (where samples are in columns):
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103
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104 +-----------+---------+---------+---------+-----+
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105 | UniqueID | sample1 | sample2 | sample3 | ... |
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106 +===========+=========+=========+=========+=====+
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107 | gene_1 | 1.2 | 3.5 | 2.9 | ... |
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108 +-----------+---------+---------+---------+-----+
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109 | gene_2 | 1.6 | 3.2 | 3.2 | ... |
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110 +-----------+---------+---------+---------+-----+
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111 | gene_3 | 1.4 | 3.0 | 3.1 | ... |
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112 +-----------+---------+---------+---------+-----+
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113 | gene_4 | 1.6 | 2.9 | 3.1 | ... |
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114 +-----------+---------+---------+---------+-----+
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115 | ... | ... | ... | ... | ... |
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116 +-----------+---------+---------+---------+-----+
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117
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118 (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.
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119
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120 (3) **Metabolomic Wide Dataset** A wide formatted metabolomic dataset that contains measurements for each sample (where samples are in columns):
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121
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122 +------------+---------+---------+---------+-----+
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123 | UniqueID | sample1 | sample2 | sample3 | ... |
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124 +============+=========+=========+=========+=====+
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125 | met_1 | 10 | 20 | 10 | ... |
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126 +------------+---------+---------+---------+-----+
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127 | met_2 | 5 | 22 | 30 | ... |
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128 +------------+---------+---------+---------+-----+
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129 | met_3 | 30 | 27 | 2 | ... |
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130 +------------+---------+---------+---------+-----+
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131 | met_4 | 32 | 17 | 8 | ... |
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132 +------------+---------+---------+---------+-----+
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133 | ... | ... | ... | ... | ... |
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134 +------------+---------+---------+---------+-----+
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135
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136 (4) **Unique Metabolite FeatureID** Name of the column in your Metabolite Wide Dataset that contains unique metabolite identifiers.
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137
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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).
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139
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140 +-----------+--------------+-------------+-----+
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141 | UniqueID | ENSEMBL_ID | Gene_Symbol | ... |
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142 +===========+==============+=============+=====+
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143 | gene_1 | ENS... | one | ... |
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144 +-----------+--------------+-------------+-----+
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145 | gene_2 | ENS... | two | ... |
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146 +-----------+--------------+-------------+-----+
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147 | gene_3 | ENS... | three | ... |
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148 +-----------+--------------+-------------+-----+
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149 | gene_4 | ENS... | four | ... |
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150 +-----------+--------------+-------------+-----+
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151 | ... | ... | ... | ... |
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152 +-----------+--------------+-------------+-----+
1
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153
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154 (6) **Correlation method** Select the correlation coefficient to be computed from the list. Pearson, kendall, or spearman are available.
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155
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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.
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157
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158 --------------------------------------------------------------------------------
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159
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160 **Output**
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161
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162 The user will obtain three outputs from the Gene - Metabolite Correlation Tool:
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163
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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).
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165
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166 +--------+------------+-------------+-----------+
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167 | Gene | Metabolite | Correlation | (p-value) |
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168 +========+============+=============+===========+
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169 | gene_1 | met_1 | 0.99 | 0.000 |
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170 +--------+------------+-------------+-----------+
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171 | gene_2 | met_4 | -0.98 | 0.000 |
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172 +--------+------------+-------------+-----------+
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173 | gene_3 | met_5 | 0.96 | 0.001 |
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174 +--------+------------+-------------+-----------+
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175 | gene_4 | met_1 | 0.95 | 0.002 |
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176 +--------+------------+-------------+-----------+
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177 | ... | ... | ... | ... |
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178 +--------+------------+-------------+-----------+
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179
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180 (2) **Correlation Matrix.** Output correlation matrix.
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181
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182 +--------+-------+-------+-------+-------+-----+
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183 | Gene | met_1 | met_2 | met_3 | met_4 | ... |
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184 +========+=======+=======+=======+=======+=====+
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185 | gene_1 | 0.99 | 0.56 | 0.25 | 0.33 | ... |
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186 +--------+-------+-------+-------+-------+-----+
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187 | gene_2 | -0.57 | 0.63 | -0.14 | 0.01 | ... |
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188 +--------+-------+-------+-------+-------+-----+
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189 | gene_3 | 0.62 | 0.96 | 0.20 | 0.32 | ... |
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190 +--------+-------+-------+-------+-------+-----+
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191 | gene_4 | 0.95 | 0.25 | 0.16 | 0.44 | ... |
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192 +--------+-------+-------+-------+-------+-----+
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193 | ... | ... | ... | ... | ... | ... |
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194 +--------+-------+-------+-------+-------+-----+
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195
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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.
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197
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198 ]]>
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199 </help>
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200 <citations>
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201 <citation type="bibtex">@ARTICLE{Kirpich17secimtools,
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202 author = {Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse, Lauren M. McIntyre},
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203 title = {SECIMTools: A suite of Metabolomics Data Analysis Tools},
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204 journal = {BMC Bioinformatics},
2
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205 year = {2018}
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206 }</citation>
2
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207 <citation type="bibtex">@article{Mor2021GaitGM,
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208 title={GAIT-GM integrative cross-omics analyses reveal cholinergic defects in a C. elegans model of Parkinson's disease},
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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},
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210 journal={BMC Genomics},
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211 year={submitted},
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212 }</citation>
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213 </citations>
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214 </tool>