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1 <tool id="protein_rna_correlation" name="protein_rna_correlation" version="0.1.0">
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2 <description>Correlation between protein and rna expression (Single Sample)</description>
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3 <requirements>
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4 <requirement type="package" version="3.3.1">r-base</requirement>
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5 <requirement type="package" version="1.18.0">bioconductor-rgalaxy</requirement>
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6 <requirement type="package" version="1.21.0">bioconductor-biocinstaller</requirement>
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7 <requirement type="package" version="1.9">rmarkdown</requirement>
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8 <requirement type="package" version="1.9">MASS</requirement>
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9 <requirement type="package" version="1.8-23">mgcv</requirement>
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10 <requirement type="package" version="0.4.1">DMwR</requirement>
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11 <requirement type="package" version="1.11.4">data.table</requirement>
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12 <requirement type="package" version="3.0.1">gplots</requirement>
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13 </requirements>
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14 <command detect_errors="exit_code" interpreter="Rscript"><![CDATA[protein_rna_correlation.r $pe_exp $ge_exp $pe_idcol $ge_idcol $pe_expcol $ge_expcol $pe_idtype $ge_idtype $organism_map $writeMapUnmap $doScale "$html_file" "$html_file.files_path"]]></command>
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15
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16 <inputs>
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17 <param name="pe_exp" type="data" format="tabular">
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18 <label>Input Protein Expression File</label>
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19 </param>
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20 <param name="pe_idcol" type="integer">
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21 <label>Column: Protein/Gene ID</label>
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22 </param>
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23 <param name="pe_expcol" type="integer">
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24 <label>Column: Protein Expression Values</label>
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25 </param>
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26
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27 <param name="ge_exp" type="data" format="tabular">
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28 <label>Input RNA Expression File</label>
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29 </param>
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30
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31 <param name="ge_idcol" type="integer">
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32 <label>Column: RNA/Gene ID</label>
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33 </param>
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34 <param name="ge_expcol" type="integer">
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35 <label>Column: RNA Expression Values</label>
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36 </param>
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37
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38 <param name="pe_idtype" type="select">
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39 <option value='ensembl' selected>Ensembl</option>
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40 <option value='uniprot'>Uniprot</option>
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41 <option value='hgnc'>HGNC</option>
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42 </param>
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43
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44 <param name="ge_idtype" type="select">
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45 <option value='ensembl' selected>Ensembl</option>
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46 <option value='uniprot'>Uniprot</option>
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47 <option value='hgnc'>HGNC</option>
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48 </param>
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49
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50 <param name="organism_map" type="data" format="tabular">
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51 <label>Biomart ID Mapping file (.map)</label>
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52 </param>
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53
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54 <!--<param name="method" type="select" label="Correlation Method">
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55 <option value="pearson" selected="true">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
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60 <param name="writeMapUnmap" type="boolean">
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61 <label>Create the list of Mapped and Unmapped Identifiers in HTML</label>
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62 </param>
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63
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64 <param name="doScale" type="boolean">
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65 <label>Scale the abundance values</label>
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66 </param>
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67
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68 </inputs>
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69
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70 <outputs>
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71 <data format="html" name="html_file" label="protein_rna_corr_${tool_name}.html"/>
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72 </outputs>
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73
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74 <tests>
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75 <test>
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76 <param name="pe_exp" value="PE_mouse_singlesample.txt"/>
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77 <param name="pe_idcol" value="7"/>
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78 <param name="ge_exp" value="GE_mouse_singlesample.txt"/>
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79 <param name="ge_idcol" value="1"/>
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80 <param name="method" value="pearson"/>
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81 <param name="pe_expcol" value="13"/>
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82 <param name="ge_expcol" value="10"/>
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83 <param name="pe_idtype" value="Ensembl_with_version"/>
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84 <param name="ge_idtype" value="Ensembl_with_version"/>
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85 <param name="organism_map" value="mmusculus_gene_ensembl__GRCm38.p6.map"/>
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86 <param name="writeMapUnmap" value="1"/>
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87 <param name="doScale" value="1"/>
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88 <output name="html_file" file="PE_abundance_GE_abundance_pearson.html"/>
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89 </test>
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90 </tests>
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91
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92 <help>
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93 Proteome Transcriptome Correlation
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94 Developer: Priyabrata Panigrahi
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95 </help>
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96 </tool>
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