|
0
|
1 <tool id="protein_rna_correlation" name="protein_rna_correlation" version="0.1.0">
|
|
|
2 <description>Correlation between protein and rna expression (Single Sample)</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="3.3.1">r-base</requirement>
|
|
|
5 <requirement type="package" version="1.18.0">bioconductor-rgalaxy</requirement>
|
|
|
6 <requirement type="package" version="1.21.0">bioconductor-biocinstaller</requirement>
|
|
|
7 <requirement type="package" version="1.9">rmarkdown</requirement>
|
|
|
8 <requirement type="package" version="1.9">MASS</requirement>
|
|
|
9 <requirement type="package" version="1.8-23">mgcv</requirement>
|
|
|
10 <requirement type="package" version="0.4.1">DMwR</requirement>
|
|
|
11 <requirement type="package" version="1.11.4">data.table</requirement>
|
|
|
12 <requirement type="package" version="3.0.1">gplots</requirement>
|
|
2
|
13 <requirement type="package" version="0.20-35">lattice</requirement>
|
|
|
14 <requirement type="package" version="3.5.0">grid</requirement>
|
|
|
15 <requirement type="package" version="3.1-137">nlme</requirement>
|
|
0
|
16 </requirements>
|
|
|
17 <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>
|
|
|
18
|
|
|
19 <inputs>
|
|
|
20 <param name="pe_exp" type="data" format="tabular">
|
|
|
21 <label>Input Protein Expression File</label>
|
|
|
22 </param>
|
|
|
23 <param name="pe_idcol" type="integer">
|
|
|
24 <label>Column: Protein/Gene ID</label>
|
|
|
25 </param>
|
|
|
26 <param name="pe_expcol" type="integer">
|
|
|
27 <label>Column: Protein Expression Values</label>
|
|
|
28 </param>
|
|
|
29
|
|
|
30 <param name="ge_exp" type="data" format="tabular">
|
|
|
31 <label>Input RNA Expression File</label>
|
|
|
32 </param>
|
|
|
33
|
|
|
34 <param name="ge_idcol" type="integer">
|
|
|
35 <label>Column: RNA/Gene ID</label>
|
|
|
36 </param>
|
|
|
37 <param name="ge_expcol" type="integer">
|
|
|
38 <label>Column: RNA Expression Values</label>
|
|
|
39 </param>
|
|
|
40
|
|
|
41 <param name="pe_idtype" type="select">
|
|
|
42 <option value='ensembl' selected>Ensembl</option>
|
|
|
43 <option value='uniprot'>Uniprot</option>
|
|
|
44 <option value='hgnc'>HGNC</option>
|
|
|
45 </param>
|
|
|
46
|
|
|
47 <param name="ge_idtype" type="select">
|
|
|
48 <option value='ensembl' selected>Ensembl</option>
|
|
|
49 <option value='uniprot'>Uniprot</option>
|
|
|
50 <option value='hgnc'>HGNC</option>
|
|
|
51 </param>
|
|
|
52
|
|
|
53 <param name="organism_map" type="data" format="tabular">
|
|
|
54 <label>Biomart ID Mapping file (.map)</label>
|
|
|
55 </param>
|
|
|
56
|
|
|
57 <!--<param name="method" type="select" label="Correlation Method">
|
|
|
58 <option value="pearson" selected="true">Pearson</option>
|
|
|
59 <option value="spearman">Spearman</option>
|
|
|
60 <option value="kendall">Kendall</option>
|
|
|
61 </param>-->
|
|
|
62
|
|
|
63 <param name="writeMapUnmap" type="boolean">
|
|
|
64 <label>Create the list of Mapped and Unmapped Identifiers in HTML</label>
|
|
|
65 </param>
|
|
|
66
|
|
|
67 <param name="doScale" type="boolean">
|
|
|
68 <label>Scale the abundance values</label>
|
|
|
69 </param>
|
|
|
70
|
|
|
71 </inputs>
|
|
|
72
|
|
|
73 <outputs>
|
|
|
74 <data format="html" name="html_file" label="protein_rna_corr_${tool_name}.html"/>
|
|
|
75 </outputs>
|
|
|
76
|
|
|
77 <tests>
|
|
|
78 <test>
|
|
|
79 <param name="pe_exp" value="PE_mouse_singlesample.txt"/>
|
|
|
80 <param name="pe_idcol" value="7"/>
|
|
|
81 <param name="ge_exp" value="GE_mouse_singlesample.txt"/>
|
|
|
82 <param name="ge_idcol" value="1"/>
|
|
|
83 <param name="method" value="pearson"/>
|
|
|
84 <param name="pe_expcol" value="13"/>
|
|
|
85 <param name="ge_expcol" value="10"/>
|
|
|
86 <param name="pe_idtype" value="Ensembl_with_version"/>
|
|
|
87 <param name="ge_idtype" value="Ensembl_with_version"/>
|
|
|
88 <param name="organism_map" value="mmusculus_gene_ensembl__GRCm38.p6.map"/>
|
|
|
89 <param name="writeMapUnmap" value="1"/>
|
|
|
90 <param name="doScale" value="1"/>
|
|
|
91 <output name="html_file" file="PE_abundance_GE_abundance_pearson.html"/>
|
|
|
92 </test>
|
|
|
93 </tests>
|
|
|
94
|
|
|
95 <help>
|
|
|
96 Proteome Transcriptome Correlation
|
|
|
97 Developer: Priyabrata Panigrahi
|
|
|
98 </help>
|
|
|
99 </tool>
|
