Mercurial > repos > galaxyp > lfq_protein_quant

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