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annotate ensembl2symbol.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
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1 <tool id="secimtools_ensembl2symbol" name="Map ENSEMBLIDs to Gene Symbols." 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 <stdio>
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8 <exit_code range="1" level="fatal" description="Repeated Unique IDs"/>
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9 </stdio>
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10 <command detect_errors="exit_code"><![CDATA[
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11 ensembl2symbol.py
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12 -s=$species
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13 -ga=$geneAnnot
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14 -id=$uniqId
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15 -e=$ensemblId
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16 -o=$output
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17 ]]></command>
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18 <inputs>
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19 <param name="species" type="select" label="Select the species your ENSEMBLIDs are from" >
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20 <option value="human">Homo sapiens</option>
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21 <option value="mouse">Mus musculus</option>
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22 <option value="rat">Rattus norvegicus</option>
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23 <option value="fruitfly">Drosophila melanogaster</option>
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24 <option value="thale-cress">Arabidopsis thaliana</option>
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25 <option value="nematode">Caenorhabditis elegans</option>
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26 </param>
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27 <param name="geneAnnot" type="data" format="tabular" label="Select the Dataset from your History containing the ENSEMBLIDs"/>
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28 <param name="uniqId" type="text" size="30" value="" label="Unique Gene FeatureID" help="Name of the column in your dataset containing unique FeatureIDs."/>
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29 <param name="ensemblId" type="text" size="30" value="" label="ENSEMBLID" help="Name of the column containing the ENSEMBLIDs to use for linking to gene symbols."/>
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30 </inputs>
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31 <outputs>
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32 <data format="tabular" name="output" label="${tool.name} on ${on_string}: ENSEMBL to GeneSymbol Annotation File"/>
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="species" value="rat"/>
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37 <param name="geneAnnot" value="gene_annotation.tsv"/>
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38 <param name="uniqId" value="UniqueID"/>
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39 <param name="ensemblId" value="GeneName"/>
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40 <output name="output" value="ensembl2symbol_annotation.tsv"/>
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41 </test>
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42 </tests>
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43 <help><![CDATA[
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44
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45 **Tool Description**
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46
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47 This tool takes an annotation data file containing unique FeatureIDs and Ensembl IDs and adds
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48 gene symbols. The link from the Ensembl IDs to gene symbols is made using mygene
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49 (https://mygene.info/). The tool adds the following columns to the input annotation data file:
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50 GeneSymbol, Score, Selected and Tie.
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51
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52 The GeneSymbol column contains the short-form abbreviation for the gene. The Score column
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53 contains a value generated by mygene indicating how well the Ensembl ID matched the returned gene
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54 symbol(s) (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0953-9). For
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55 cases where an Ensembl ID uniquely matches to a gene symbol, the Selected column = ‘Yes”. For
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56 cases where an Ensembl ID matches to more than one gene symbol, the Selected column = ‘Yes’ for
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57 the gene symbol with the best Score value. If there is a tie, the alphabetically first gene
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58 symbol is selected and the Tie column = ‘Yes’. We note that FeatureID may not be unique in the
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59 resulting output dataset.
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60
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61 --------------------------------------------------------------------------------
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62
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63 **Input**
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64
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65 **Dataset with unique FeatureID and ENSEMBLID values**
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66
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67 +-------------+--------------+-----+
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68 | FeatureID | ENSEMBLID | ... |
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69 +=============+==============+=====+
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70 | FeatureID_1 | ENS... | ... |
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71 +-------------+--------------+-----+
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72 | FeatureID_2 | ENS... | ... |
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73 +-------------+--------------+-----+
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74 | FeatureID_3 | ENS... | ... |
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75 +-------------+--------------+-----+
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76 | ... | ... | ... |
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77 +-------------+--------------+-----+
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78
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79 **NOTE:** This file must contain at least two columns, a column with unique FeatureIDs and a column containing ENSEMBLIDs. Other columns may be present.
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80
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81 **Unique FeatureID**
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82
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83 Name of the column in your input dataset that has unique FeatureIDs.
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84
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85 **ENSEMBLID**
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86
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87 Name of the column containing the ENSEMBLIDs.
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88
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89 --------------------------------------------------------------------------------
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90
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91 **OUTPUT**
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92
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93 The user will get a single output file containing the linked gene symbols.
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94
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95 **Output Table**
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96
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97 +-------------+------------+--------------+-------------+-----------+----------+
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98 | FeatureID | ENSEMBLID | ... | GeneSymbol | Score | Selected |
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99 +=============+============+==============+=============+===========+==========+
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100 | FeatureID_1 | ENS... | ... | one* | 13.550056 | Yes |
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101 +-------------+------------+--------------+-------------+-----------+----------+
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102 | FeatureID_2 | ENS... | ... | two* | 12.984067 | Yes |
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103 +-------------+------------+--------------+-------------+-----------+----------+
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104 | FeatureID_2 | ENS... | ... | three* | 11.995048 | No |
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105 +-------------+------------+--------------+-------------+-----------+----------+
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106 | FeatureID_3 | ENS... | ... | four* | 12.549084 | Yes |
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107 +-------------+------------+--------------+-------------+-----------+----------+
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108 | ... | ... | ... | ... | ... | ... |
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109 +-------------+------------+--------------+-------------+-----------+----------+
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110
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111 '*'=refers to the matched gene
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112
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113 ]]></help>
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114 <citations>
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115 <citation type="bibtex">@ARTICLE{Kirpich17secimtools,
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116 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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117 title = {SECIMTools: A suite of Metabolomics Data Analysis Tools},
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118 journal = {BMC Bioinformatics},
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119 year = {2018}
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120 }</citation>
2
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121 <citation type="bibtex">@article{Mor2021GaitGM,
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122 title={GAIT-GM integrative cross-omics analyses reveal cholinergic defects in a C. elegans model of Parkinson's disease},
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123 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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124 journal={BMC Genomics},
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125 year={submitted},
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126 }</citation>
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127 <citation type="bibtex">@article{xim2016mygene,
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128 title={High-performance web services for querying gene and variant annotation},
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129 author={Xin, J and Mark, A and Afrashiabi, C and Tsueng, G and Juchler, M and Gopal, N and Stupp, GS and Putman, TE and Ainscough, BJ and Griffith, OL and Torkamani, A and Whetzel, PL and Mungall, CJ and Mooney, SD and Su, AI and Wu, C},
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130 journal={Genome Biology},
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131 year={2016},
1
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132 }</citation>
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133 </citations>
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134 </tool>