Mercurial > repos > pravs > protein_rna_correlation

comparison protein_rna_correlation.xml @ 5:6bf0203ee17e draft

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planemo upload
author pravs
date Wed, 20 Jun 2018 20:43:56 -0400
parents b014014e685a
children 8e9428eca82c
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4:b014014e685a 5:6bf0203ee17e
1 <tool id="protein_rna_correlation" name="protein_rna_correlation" version="0.1.1"> 1 <tool id="protein_rna_correlation" name="protein_rna_correlation" version="0.0.2">
2 <description>Correlation between protein and rna expression (Single Sample)</description> 2 <description>Correlation between protein and transcript expression </description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.3.1">r-base</requirement> 4 <requirement type="package" version="3.2.1">R</requirement>
5 <requirement type="package" version="1.18.0">bioconductor-rgalaxy</requirement> 5 <requirement type="package" version="0.0.1">r-protrnacorr</requirement>
6 <requirement type="package" version="1.21.0">bioconductor-biocinstaller</requirement> 6 <requirement type="package" version="1.5.0">x11</requirement>
7 <requirement type="package" version="1.9">rmarkdown</requirement> 7
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 <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>
16 </requirements> 8 </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> 9 <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 <inputs> 10 <inputs>
19 <param name="pe_exp" type="data" format="tabular"> 11 <param name="pe_exp" type="data" format="tabular">
20 <label>Input Protein Expression File</label> 12 <label>Input Protein Expression File</label>
21 </param> 13 </param>
22 <param name="pe_idcol" type="integer"> 14 <param name="pe_idcol" type="integer" value="1">
23 <label>Column: Protein/Gene ID</label> 15 <label>Column: Protein/Gene ID</label>
24 </param> 16 </param>
25 <param name="pe_expcol" type="integer"> 17 <param name="pe_expcol" type="integer" value="1">
26 <label>Column: Protein Expression Values</label> 18 <label>Column: Protein Expression Values</label>
27 </param> 19 </param>
28 20
29 <param name="ge_exp" type="data" format="tabular"> 21 <param name="ge_exp" type="data" format="tabular">
30 <label>Input RNA Expression File</label> 22 <label>Input RNA Expression File</label>
31 </param> 23 </param>
32 24
33 <param name="ge_idcol" type="integer"> 25 <param name="ge_idcol" type="integer" value="1">
34 <label>Column: RNA/Gene ID</label> 26 <label>Column: RNA/Gene ID</label>
35 </param> 27 </param>
36 <param name="ge_expcol" type="integer"> 28 <param name="ge_expcol" type="integer" value="1">
37 <label>Column: RNA Expression Values</label> 29 <label>Column: RNA Expression Values</label>
38 </param> 30 </param>
39 31
40 <param name="pe_idtype" type="select"> 32 <param name="pe_idtype" type="select" label="Protein ID type">
41 <option value='ensembl' selected>Ensembl</option> 33 <option value="Ensembl_with_version" selected="True">Ensembl</option>
42 <option value='uniprot'>Uniprot</option> 34 <option value="uniprot">Uniprot</option>
43 <option value='hgnc'>HGNC</option> 35 <option value="hgnc">HGNC</option>
44 </param> 36 </param>
45 37
46 <param name="ge_idtype" type="select"> 38 <param name="ge_idtype" type="select" label="Transcript ID type">
47 <option value='ensembl' selected>Ensembl</option> 39 <option value="Ensembl_with_version" selected="True">Ensembl</option>
48 <option value='uniprot'>Uniprot</option> 40 <option value="uniprot">Uniprot</option>
49 <option value='hgnc'>HGNC</option> 41 <option value="hgnc">HGNC</option>
50 </param> 42 </param>
51 43
52 <param name="organism_map" type="data" format="tabular"> 44 <param name="organism_map" type="data" format="tabular">
53 <label>Biomart ID Mapping file (.map)</label> 45 <label>Biomart ID Mapping file (.map)</label>
54 </param> 46 </param>
55 47
56 <param name="writeMapUnmap" type="boolean"> 48 <param name="writeMapUnmap" type="boolean" checked="true" truevalue="1" falsevalue="0">
57 <label>Create the list of Mapped and Unmapped Identifiers in HTML</label> 49 <label>Create the list of Mapped and Unmapped Identifiers in HTML</label>
58 </param> 50 </param>
59 51
60 <param name="doScale" type="boolean"> 52 <param name="doScale" type="boolean" checked="true" truevalue="1" falsevalue="0">
61 <label>Scale the abundance values</label> 53 <label>Scale the abundance values</label>
62 </param> 54 </param>
63 55
64 </inputs> 56 </inputs>
65 57
66 <outputs> 58 <outputs>
67 <data format="html" name="html_file" label="protein_rna_corr_${tool_name}.html"/> 59 <data format="html" name="html_file" label="protein_rna_corr_${tool.name}.html"/>
68 </outputs> 60 </outputs>
69 61
70 <tests> 62 <tests>
71 <test> 63 <test>
72 <param name="pe_exp" value="PE_mouse_singlesample.txt"/> 64 <param name="pe_exp" value="PE_mouse_singlesample.txt"/>
76 <param name="pe_expcol" value="13"/> 68 <param name="pe_expcol" value="13"/>
77 <param name="ge_expcol" value="10"/> 69 <param name="ge_expcol" value="10"/>
78 <param name="pe_idtype" value="Ensembl_with_version"/> 70 <param name="pe_idtype" value="Ensembl_with_version"/>
79 <param name="ge_idtype" value="Ensembl_with_version"/> 71 <param name="ge_idtype" value="Ensembl_with_version"/>
80 <param name="organism_map" value="mmusculus_gene_ensembl__GRCm38.p6.map"/> 72 <param name="organism_map" value="mmusculus_gene_ensembl__GRCm38.p6.map"/>
81 <param name="writeMapUnmap" value="1"/> 73 <param name="writeMapUnmap" value="true"/>
82 <param name="doScale" value="1"/> 74 <param name="doScale" value="true"/>
83 <output name="html_file" file="PE_abundance_GE_abundance_pearson.html"/> 75 <output name="html_file" file="protein_rna_corr_protein_transcript_correlation.html"/>
84 </test> 76 </test>
85 </tests> 77 </tests>
86 78
87 <help> 79 <help><![CDATA[
88 Proteome Transcriptome Correlation 80 Proteome Transcriptome Correlation
89 Developer: Priyabrata Panigrahi 81 Developer: Priyabrata Panigrahi
90 </help> 82 ]]></help>
83 <citations>
84 <citation type="bibtex">
85 @misc{protein_rna_correlation,
86 author={Panigrahi, Priyabrata},
87 year={2018},
88 title={ProteinRNACorrelation}
89 }
90 </citation>
91 </citations>
91 </tool> 92 </tool>