|
5
|
1 <tool id="protein_rna_correlation" name="protein_rna_correlation" version="0.0.2">
|
|
|
2 <description>Correlation between protein and transcript expression </description>
|
|
0
|
3 <requirements>
|
|
5
|
4 <requirement type="package" version="3.2.1">R</requirement>
|
|
|
5 <requirement type="package" version="0.0.1">r-protrnacorr</requirement>
|
|
6
|
6 <!--<requirement type="package" version="1.5.0">x11</requirement>-->
|
|
0
|
7 </requirements>
|
|
4
|
8 <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>
|
|
0
|
9 <inputs>
|
|
|
10 <param name="pe_exp" type="data" format="tabular">
|
|
|
11 <label>Input Protein Expression File</label>
|
|
|
12 </param>
|
|
5
|
13 <param name="pe_idcol" type="integer" value="1">
|
|
0
|
14 <label>Column: Protein/Gene ID</label>
|
|
|
15 </param>
|
|
5
|
16 <param name="pe_expcol" type="integer" value="1">
|
|
0
|
17 <label>Column: Protein Expression Values</label>
|
|
|
18 </param>
|
|
|
19
|
|
|
20 <param name="ge_exp" type="data" format="tabular">
|
|
|
21 <label>Input RNA Expression File</label>
|
|
|
22 </param>
|
|
|
23
|
|
5
|
24 <param name="ge_idcol" type="integer" value="1">
|
|
0
|
25 <label>Column: RNA/Gene ID</label>
|
|
|
26 </param>
|
|
5
|
27 <param name="ge_expcol" type="integer" value="1">
|
|
0
|
28 <label>Column: RNA Expression Values</label>
|
|
|
29 </param>
|
|
|
30
|
|
5
|
31 <param name="pe_idtype" type="select" label="Protein ID type">
|
|
|
32 <option value="Ensembl_with_version" selected="True">Ensembl</option>
|
|
|
33 <option value="uniprot">Uniprot</option>
|
|
|
34 <option value="hgnc">HGNC</option>
|
|
0
|
35 </param>
|
|
|
36
|
|
5
|
37 <param name="ge_idtype" type="select" label="Transcript ID type">
|
|
|
38 <option value="Ensembl_with_version" selected="True">Ensembl</option>
|
|
|
39 <option value="uniprot">Uniprot</option>
|
|
|
40 <option value="hgnc">HGNC</option>
|
|
0
|
41 </param>
|
|
|
42
|
|
|
43 <param name="organism_map" type="data" format="tabular">
|
|
|
44 <label>Biomart ID Mapping file (.map)</label>
|
|
|
45 </param>
|
|
|
46
|
|
5
|
47 <param name="writeMapUnmap" type="boolean" checked="true" truevalue="1" falsevalue="0">
|
|
0
|
48 <label>Create the list of Mapped and Unmapped Identifiers in HTML</label>
|
|
|
49 </param>
|
|
|
50
|
|
5
|
51 <param name="doScale" type="boolean" checked="true" truevalue="1" falsevalue="0">
|
|
0
|
52 <label>Scale the abundance values</label>
|
|
|
53 </param>
|
|
|
54
|
|
|
55 </inputs>
|
|
|
56
|
|
|
57 <outputs>
|
|
5
|
58 <data format="html" name="html_file" label="protein_rna_corr_${tool.name}.html"/>
|
|
0
|
59 </outputs>
|
|
|
60
|
|
|
61 <tests>
|
|
|
62 <test>
|
|
|
63 <param name="pe_exp" value="PE_mouse_singlesample.txt"/>
|
|
|
64 <param name="pe_idcol" value="7"/>
|
|
|
65 <param name="ge_exp" value="GE_mouse_singlesample.txt"/>
|
|
|
66 <param name="ge_idcol" value="1"/>
|
|
|
67 <param name="pe_expcol" value="13"/>
|
|
|
68 <param name="ge_expcol" value="10"/>
|
|
|
69 <param name="pe_idtype" value="Ensembl_with_version"/>
|
|
|
70 <param name="ge_idtype" value="Ensembl_with_version"/>
|
|
|
71 <param name="organism_map" value="mmusculus_gene_ensembl__GRCm38.p6.map"/>
|
|
5
|
72 <param name="writeMapUnmap" value="true"/>
|
|
|
73 <param name="doScale" value="true"/>
|
|
|
74 <output name="html_file" file="protein_rna_corr_protein_transcript_correlation.html"/>
|
|
0
|
75 </test>
|
|
|
76 </tests>
|
|
|
77
|
|
5
|
78 <help><![CDATA[
|
|
0
|
79 Proteome Transcriptome Correlation
|
|
|
80 Developer: Priyabrata Panigrahi
|
|
5
|
81 ]]></help>
|
|
|
82 <citations>
|
|
|
83 <citation type="bibtex">
|
|
|
84 @misc{protein_rna_correlation,
|
|
|
85 author={Panigrahi, Priyabrata},
|
|
|
86 year={2018},
|
|
|
87 title={ProteinRNACorrelation}
|
|
|
88 }
|
|
|
89 </citation>
|
|
|
90 </citations>
|
|
0
|
91 </tool>
|
