Mercurial > repos > galaxyp > lfq_protein_quant
comparison lfq_protein_quant.xml @ 0:bb199421f731 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant commit 26ff08776f90f96646598a19cfcf57d42aa4a43b
author | galaxyp |
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date | Tue, 02 Oct 2018 16:30:33 -0400 |
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1 <tool id="lfq_protein_quant" name="Label free protein" version="1.0"> | |
2 <description> | |
3 summarisation and quantitation | |
4 </description> | |
5 <requirements> | |
6 <requirement type="package" version="2.2.0">bioconductor-msnbase</requirement> | |
7 <requirement type="package" version="2.12.0">bioconductor-mzr</requirement> | |
8 <requirement type="package" version="1.2.1">r-tidyverse</requirement> | |
9 <requirement type="package" version="1.1_18_1">r-lme4</requirement> | |
10 <requirement type="package" version="0.1.0">r-furrr</requirement> | |
11 <requirement type="package" version="0.7.5">r-msqrob</requirement> | |
12 </requirements> | |
13 <command detect_errors="exit_code"> | |
14 <![CDATA[ | |
15 ln -s '${moff_file}' moff.tsv && | |
16 ln -s '${meta_file}' meta.tsv && | |
17 Rscript '$__tool_directory__/quantitation.r' | |
18 moff.tsv | |
19 meta.tsv | |
20 $only_summarisation | |
21 \${GALAXY_SLOTS:-4} | |
22 ]]> | |
23 </command> | |
24 <inputs> | |
25 <param name="moff_file" type="data" format="tabular" | |
26 label="Peptide summary output from moFF or other peptide quantitation tools" /> | |
27 <param name="meta_file" type="data" format="tabular" label="Metadata with sample names and condition" /> | |
28 <param name="only_summarisation" type="boolean" truevalue="1" falsevalue="0" | |
29 label="Only summarisiation" help="This option will deactivate the quantifiation of data." /> | |
30 | |
31 </inputs> | |
32 <outputs> | |
33 <data format="tabular" name="quant" from_work_dir="quantitation.tsv" label="${tool.name} on ${on_string}: quantification"> | |
34 <filter>not only_summarisation</filter> | |
35 </data> | |
36 <data format="tabular" name="summary" from_work_dir="summarised_proteins.tsv" label="${tool.name} on ${on_string}: summary"/> | |
37 </outputs> | |
38 <tests> | |
39 <test> | |
40 <param name="moff_file" value="moff.tab"/> | |
41 <param name="meta_file" value="meta.tab"/> | |
42 <param name="only_summerisation" value="true"/> | |
43 <output name="quant" file="quantitation.tsv" /> | |
44 <output name="summary" file="summarised_proteins.tsv" /> | |
45 </test> | |
46 </tests> | |
47 <help> | |
48 <![CDATA[ | |
49 **What it does** | |
50 | |
51 Protein summarisation and label free quantitation. | |
52 | |
53 ---- | |
54 | |
55 **Inputs** | |
56 | |
57 - Quantification input: Tabular file with the summary output from moFF or in case other tools were used for peptide quantitation with the following columns: 'peptides' containing the amino acid sequence; 'prot' with the Uniprot Accession and then one column per sample with the quantitation values. | |
58 | |
59 :: | |
60 | |
61 peptides prot sample1 sample2 | |
62 AAABDEK B9DM54 1809446 563862 | |
63 TELATASDR Q9CFE8 294282 457023 | |
64 AMGLATK P85660 194023 428277 | |
65 ... | |
66 ... | |
67 | |
68 | |
69 - Metadata input: Separate columns with sample names, condition and optionally also lab and machine. Sample names must match exactly the sample names from the peptide quantitation columns in the previous tabular file. | |
70 | |
71 | |
72 :: | |
73 | |
74 sample condition | |
75 sample1 healthy | |
76 sample2 disease | |
77 ... | |
78 ... | |
79 | |
80 | |
81 **Options** | |
82 | |
83 - Summarisation only: Summarisation is done through robust regression to take also the peptide effect into account. In case only sample column is provided median protein intensity is calculated. | |
84 - Summarisation and quantification: Relative quantification is performed according to the information provided in the metadata file. | |
85 | |
86 | |
87 **Outputs** | |
88 | |
89 - Summarised protein output: Uniprot accession and quantitation values per sample and protein | |
90 - Quantification output: Uniprot accession, comparison between conditions, fold change, p-value, q-value | |
91 | |
92 ]]> | |
93 </help> | |
94 <citations> | |
95 <citation type="doi">10.1074/mcp.M115.055897</citation> | |
96 <citation type="doi">10.1093/bioinformatics/btr645</citation> | |
97 </citations> | |
98 </tool> |