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
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>