Mercurial > repos > pravs > protein_rna_correlation
comparison protein_rna_correlation.xml @ 0:fc89f8c3b777 draft
planemo upload
author | pravs |
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date | Sun, 17 Jun 2018 04:20:06 -0400 |
parents | |
children | 412403eec79c |
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-1:000000000000 | 0:fc89f8c3b777 |
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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> | |
13 </requirements> | |
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" "$html_file.files_path"]]></command> | |
15 | |
16 <inputs> | |
17 <param name="pe_exp" type="data" format="tabular"> | |
18 <label>Input Protein Expression File</label> | |
19 </param> | |
20 <param name="pe_idcol" type="integer"> | |
21 <label>Column: Protein/Gene ID</label> | |
22 </param> | |
23 <param name="pe_expcol" type="integer"> | |
24 <label>Column: Protein Expression Values</label> | |
25 </param> | |
26 | |
27 <param name="ge_exp" type="data" format="tabular"> | |
28 <label>Input RNA Expression File</label> | |
29 </param> | |
30 | |
31 <param name="ge_idcol" type="integer"> | |
32 <label>Column: RNA/Gene ID</label> | |
33 </param> | |
34 <param name="ge_expcol" type="integer"> | |
35 <label>Column: RNA Expression Values</label> | |
36 </param> | |
37 | |
38 <param name="pe_idtype" type="select"> | |
39 <option value='ensembl' selected>Ensembl</option> | |
40 <option value='uniprot'>Uniprot</option> | |
41 <option value='hgnc'>HGNC</option> | |
42 </param> | |
43 | |
44 <param name="ge_idtype" type="select"> | |
45 <option value='ensembl' selected>Ensembl</option> | |
46 <option value='uniprot'>Uniprot</option> | |
47 <option value='hgnc'>HGNC</option> | |
48 </param> | |
49 | |
50 <param name="organism_map" type="data" format="tabular"> | |
51 <label>Biomart ID Mapping file (.map)</label> | |
52 </param> | |
53 | |
54 <!--<param name="method" type="select" label="Correlation Method"> | |
55 <option value="pearson" selected="true">Pearson</option> | |
56 <option value="spearman">Spearman</option> | |
57 <option value="kendall">Kendall</option> | |
58 </param>--> | |
59 | |
60 <param name="writeMapUnmap" type="boolean"> | |
61 <label>Create the list of Mapped and Unmapped Identifiers in HTML</label> | |
62 </param> | |
63 | |
64 <param name="doScale" type="boolean"> | |
65 <label>Scale the abundance values</label> | |
66 </param> | |
67 | |
68 </inputs> | |
69 | |
70 <outputs> | |
71 <data format="html" name="html_file" label="protein_rna_corr_${tool_name}.html"/> | |
72 </outputs> | |
73 | |
74 <tests> | |
75 <test> | |
76 <param name="pe_exp" value="PE_mouse_singlesample.txt"/> | |
77 <param name="pe_idcol" value="7"/> | |
78 <param name="ge_exp" value="GE_mouse_singlesample.txt"/> | |
79 <param name="ge_idcol" value="1"/> | |
80 <param name="method" value="pearson"/> | |
81 <param name="pe_expcol" value="13"/> | |
82 <param name="ge_expcol" value="10"/> | |
83 <param name="pe_idtype" value="Ensembl_with_version"/> | |
84 <param name="ge_idtype" value="Ensembl_with_version"/> | |
85 <param name="organism_map" value="mmusculus_gene_ensembl__GRCm38.p6.map"/> | |
86 <param name="writeMapUnmap" value="1"/> | |
87 <param name="doScale" value="1"/> | |
88 <output name="html_file" file="PE_abundance_GE_abundance_pearson.html"/> | |
89 </test> | |
90 </tests> | |
91 | |
92 <help> | |
93 Proteome Transcriptome Correlation | |
94 Developer: Priyabrata Panigrahi | |
95 </help> | |
96 </tool> |