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1 <tool id="protein_rna_correlation" name="protein_rna_correlation" version="0.0.2">
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2 <description>Correlation between protein and transcript expression </description>
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3 <requirements>
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4 <requirement type="package" version="3.2.1">R</requirement>
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5 <requirement type="package" version="0.0.1">r-protrnacorr</requirement>
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6 <requirement type="package" version="9.10">ghostscript</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code" interpreter="Rscript"><![CDATA[
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9 protein_rna_correlation.r
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10 $pe_exp
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11 $ge_exp
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12 $pe_idcol
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13 $ge_idcol
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14 $pe_expcol
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15 $ge_expcol
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16 $pe_idtype
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17 $ge_idtype
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18 $organism_map
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19 $writeMapUnmap
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20 $doScale
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21 $html_file
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22 $html_file.files_path]]>
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23 </command>
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24 <inputs>
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25 <param name="pe_exp" type="data" format="tabular">
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26 <label>Input Protein Expression File</label>
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27 </param>
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28 <param name="pe_idcol" type="integer" value="1">
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29 <label>Column: Protein/Gene ID</label>
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30 </param>
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31 <param name="pe_expcol" type="integer" value="1">
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32 <label>Column: Protein Expression Values</label>
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33 </param>
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34
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35 <param name="ge_exp" type="data" format="tabular">
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36 <label>Input RNA Expression File</label>
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37 </param>
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38
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39 <param name="ge_idcol" type="integer" value="1">
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40 <label>Column: RNA/Gene ID</label>
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41 </param>
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42 <param name="ge_expcol" type="integer" value="1">
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43 <label>Column: RNA Expression Values</label>
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44 </param>
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45
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46 <param name="pe_idtype" type="select" label="Protein ID type">
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47 <option value="Ensembl_with_version" selected="True">Ensembl</option>
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48 <option value="uniprot">Uniprot</option>
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49 <option value="hgnc">HGNC</option>
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50 </param>
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51
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52 <param name="ge_idtype" type="select" label="Transcript ID type">
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53 <option value="Ensembl_with_version" selected="True">Ensembl</option>
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54 <option value="uniprot">Uniprot</option>
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55 <option value="hgnc">HGNC</option>
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56 </param>
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57
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58 <param name="organism_map" type="data" format="tabular">
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59 <label>Biomart ID Mapping file (.map)</label>
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60 </param>
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61
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62 <param name="writeMapUnmap" type="boolean" checked="true" truevalue="1" falsevalue="0">
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63 <label>Create the list of Mapped and Unmapped Identifiers in HTML</label>
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64 </param>
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65
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66 <param name="doScale" type="boolean" checked="true" truevalue="1" falsevalue="0">
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67 <label>Scale the abundance values</label>
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68 </param>
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69
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70 </inputs>
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71
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72 <outputs>
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73 <data format="html" name="html_file" label="protein_rna_corr_${tool.name}.html"/>
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74 </outputs>
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75
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76 <tests>
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77 <test>
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78 <param name="pe_exp" value="PE_mouse_singlesample.txt"/>
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79 <param name="pe_idcol" value="7"/>
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80 <param name="ge_exp" value="GE_mouse_singlesample.txt"/>
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81 <param name="ge_idcol" value="1"/>
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82 <param name="pe_expcol" value="13"/>
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83 <param name="ge_expcol" value="10"/>
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84 <param name="pe_idtype" value="Ensembl_with_version"/>
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85 <param name="ge_idtype" value="Ensembl_with_version"/>
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86 <param name="organism_map" value="mmusculus_gene_ensembl__GRCm38.p6.map"/>
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87 <param name="writeMapUnmap" value="true"/>
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88 <param name="doScale" value="true"/>
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89 <output name="html_file" file="protein_rna_corr_protein_transcript_correlation.html"/>
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90 </test>
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91 </tests>
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92
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93 <help><![CDATA[
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94 Proteome Transcriptome Correlation
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95 Developer: Priyabrata Panigrahi
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96 ]]></help>
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97 <citations>
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98 <citation type="bibtex">
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99 @misc{protein_rna_correlation,
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100 author={Panigrahi, Priyabrata},
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101 year={2018},
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102 title={ProteinRNACorrelation}
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103 }
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104 </citation>
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105 </citations>
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106 </tool>
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