comparison protein_rna_correlation.xml @ 0:fc89f8c3b777 draft

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author pravs
date Sun, 17 Jun 2018 04:20:06 -0400
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children 412403eec79c
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-1:000000000000 0:fc89f8c3b777
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>