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annotate mqppep_anova.xml @ 13:b41a077af3aa draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
author eschen42
date Tue, 22 Mar 2022 20:47:40 +0000
parents 4deacfee76ef
children 2c5f1a2fe16a
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c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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1 <tool id="mqppep_anova" name="MaxQuant Phosphopeptide ANOVA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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2 <description>Perform ANOVA on merged and filtered data from phospho-peptide enrichment/MaxQuant pipeline</description>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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3 <macros>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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4 <import>macros.xml</import>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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5 </macros>
7
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6 <expand macro="requirements"/>
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7 <!--
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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8 The weird invocation used here is because knitr and install_tinytex
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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9 both need access to a writeable directory, but most directories in a
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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10 biocontainer are read-only, so this builds a pseudo-home under /tmp
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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11 -->
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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12 <command detect_errors="exit_code"><![CDATA[
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d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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13 export OLD_PWD=\$(dirname \$(pwd));
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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14 export HOME=/tmp\${OLD_PWD};
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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15 mkdir -p \$HOME/bin;
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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16 mkdir -p \$HOME/tmp;
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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17 export TEMP=\$HOME/tmp;
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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18 export TMPDIR=\$TEMP;
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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19 cd \$TEMP;
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20 cp '$__tool_directory__/mqppep_anova_script.Rmd' . || exit 0;
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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21 cp '$__tool_directory__/mqppep_anova.R' . || exit 0;
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b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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22 \${CONDA_PREFIX}/bin/Rscript \$TEMP/mqppep_anova.R
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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23 --inputFile '$input_file'
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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24 --alphaFile '$alpha_file'
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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25 --firstDataColumn $first_data_column
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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26 --imputationMethod $imputation.imputation_method
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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27 #if $imputation.imputation_method == "random"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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28 --meanPercentile '$imputation.meanPercentile'
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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29 --sdPercentile '$imputation.sdPercentile'
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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30 #end if
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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31 --regexSampleNames $sample_names_regex_f
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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32 --regexSampleGrouping $sample_grouping_regex_f
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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33 --imputedDataFile $imputed_data_file
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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34 --imputedQNLTDataFile '$imp_qn_lt_file'
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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35 --reportFile '$report_file';
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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36 export RESULT=\$?;
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37 cd \${OLD_PWD};
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b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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38 rm -rf \$HOME;
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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39 exit \${RESULT}
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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40 ]]></command>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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41 <configfiles>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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42 <configfile name="sample_names_regex_f">
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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43 $sample_names_regex
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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44 </configfile>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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45 <configfile name="sample_grouping_regex_f">
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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46 $sample_grouping_regex
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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47 </configfile>
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48 </configfiles>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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49 <inputs>
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50 <param name="input_file" type="data" format="tabular" label="Filtered Phosphopeptide Intensities"
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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51 help="[input_file] Phosphopeptide intensities filtered for minimal quality. First column label 'Phosphopeptide'; sample-intensities must begin in column 10 and must have column labels to match argument [sample_names_regex]"
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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52 />
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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53 <param name="alpha_file" type="data" format="tabular" label="alpha cutoff level"
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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54 help="[alpha_file] List of alpha cutoff values for significance testing; text file having one column and no header"
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55 />
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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56 <param name="first_data_column" type="text" value="Intensity"
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57 label="First data column"
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58 help="[first_data_column] First column having intensity values (integer or PERL-compatible regular expression matching column label)"
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59 />
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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60 <!-- imputation_method <- c("group-median","median","mean","random")[1] -->
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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61 <conditional name="imputation">
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62 <param name="imputation_method" type="select" label="Imputation Method"
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63 help="[imputation_method] Impute missing values by (1) using median for each sample-group; (2) using median across all samples; (3) using mean across all samples; or (4) using randomly generated values having same std. dev. as across all samples (with mean specified by [meanPercentile])"
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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64 >
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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65 <option value="random" selected="true">random</option>
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66 <option value="group-median">group-median</option>
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67 <option value="median">median</option>
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68 <option value="mean">mean</option>
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69 </param>
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70 <when value="group-median" />
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71 <when value="median" />
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72 <when value="mean" />
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73 <when value="random">
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74 <param name="meanPercentile" type="integer" value="1" min="1" max="99"
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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75 label="Mean percentile for random values"
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76 help="[meanPercentile] Percentile center of random values; range [1,99]"
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77 />
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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78 <param name="sdPercentile" type="float" value="0.2"
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79 label="Percentile std. dev. for random values"
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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80 help="[sdPercentile] Standard deviation adjustment-factor for random values; real number. (1.0 means SD equal to the SD for the entire data set.)"
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81 />
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82 </when>
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83 </conditional>
12
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84 <param name="sample_names_regex" type="text" value="\.\d+[A-Z]$"
0
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85 help="[sample_names_regex] PERL-compatible regular expression extracting sample-names from the the name of a spectrum file (without extension)"
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86 label="Sample-extraction regex">
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87 <sanitizer>
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88 <valid initial="string.printable">
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89 <remove value="&apos;"/>
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90 </valid>
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91 </sanitizer>
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92 </param>
12
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93 <param name="sample_grouping_regex" type="text" value="\d+"
0
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94 help="[sample_grouping_regex] PERL-compatible regular expression extracting sample-group from each sample-name (i.e., extracted by previous regex pattern)"
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95 label="Group-extraction regex">
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96 <sanitizer>
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97 <valid initial="string.printable">
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98 <remove value="&apos;"/>
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99 </valid>
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100 </sanitizer>
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101 </param>
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102 </inputs>
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103 <outputs>
13
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104 <data name="imputed_data_file" format="tabular" label="${input_file.name}.${imputation.imputation_method}-imputed_intensities" ></data>
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105 <data name="imp_qn_lt_file" format="tabular" label="${input_file.name}.${imputation.imputation_method}-imputed_QN_LT_intensities" ></data>
7
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106 <!--
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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107 <data name="report_file" format="html" label="${input_file.name}.${imputation.imputation_method}-imputed_report (download/unzip to view)" ></data>
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108 -->
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109 <data name="report_file" format="pdf" label="${input_file.name}.${imputation.imputation_method}-imputed_report" ></data>
0
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110 </outputs>
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111 <tests>
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112 <test>
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113 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
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114 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
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115 <param name="first_data_column" value="10"/>
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116 <param name="imputation_method" value="group-median"/>
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117 <param name="sample_names_regex" value="\.\d+[A-Z]$"/>
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118 <param name="sample_grouping_regex" value="\d+"/>
13
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119 <output name="imp_qn_lt_file">
0
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120 <assert_contents>
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121 <has_text text="Phosphopeptide" />
5
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122 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
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123 <has_text text="7.935878" />
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124 <has_text text="pSQKQEEENPAEETGEEK" />
0
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125 </assert_contents>
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126 </output>
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127 </test>
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128 <test>
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129 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
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130 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
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131 <param name="first_data_column" value="10"/>
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132 <param name="imputation_method" value="random"/>
7
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133 <param name="meanPercentile" value="1" />
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134 <param name="sdPercentile" value="0.2" />
0
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135 <param name="sample_names_regex" value="\.\d+[A-Z]$"/>
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136 <param name="sample_grouping_regex" value="\d+"/>
13
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137 <output name="imp_qn_lt_file">
0
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138 <assert_contents>
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139 <has_text text="Phosphopeptide" />
5
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140 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
13
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141 <has_text text="8.392287" />
5
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142 <has_text text="pSQKQEEENPAEETGEEK" />
0
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143 </assert_contents>
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144 </output>
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145 </test>
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146 </tests>
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147 <help><![CDATA[
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148 ===========================================
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149 Phopsphoproteomic Enrichment Pipeline ANOVA
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150 ===========================================
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151
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152 **Input files**
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153
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154 ``input_file``
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155 Phosphopeptides annotated with SwissProt and phosphosite metadata (in tabular format).
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156 This is the output from the "Phopsphoproteomic Enrichment Pipeline Merge and Filter"
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157 (``mqppep_mrgflt``) tool.
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158
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159 ``alpha_file``
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160 List of alpha cutoff values for significance testing; text file having one column and no header. For example:
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161
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162 ::
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163
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164 0.2
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165 0.1
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166 0.05
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167
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168 **Input parameters**
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169
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170 ``first_data_column``
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171 First column of ``input_file`` having intensity values (integer or PERL-compatible regular expression matching column label). Default: **Intensity**
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172
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173 ``imputation_method``
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174 Impute missing values by:
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175
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176 1. using median for each sample-group;
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177 2. using median across all samples;
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178 3. using mean across all samples; or
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179 4. using randomly generated values where:
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180
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181 - ``meanPercentile`` specifies the percentile among non-missing values to be used as mean of random values, and
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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182 - ``sdPercentile`` specifies the factor to be mulitplied by the standard deviation among the non-missing values (across all samples) to determine the standard deviation of random values.
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183
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184 ``sample_names_regex``
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185 PERL-compatible regular expression extracting the sample-name from the the name of a column of instensities (from ``input_file``) for one sample.
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186
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187 - For example, ``"\.\d+[A-Z]$"`` applied to ``Intensity.splunge.10A`` would produce ``.10A``
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188 - Note that *this is case sensitive* by default.
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189
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190 ``sample_grouping_regex``
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191 PERL-compatible regular expression extracting the sample-grouping from the sample-name that was extracted with ``sample_names_regex`` from a column of intensites (from ``input_file``).
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192
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193 - For example, ``"\d+$"`` applied to ``.10A`` would produce ``10``
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194 - Note that *this is case sensitive* by default.
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195
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196
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197 **Outputs**
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198
13
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199 ``imputed_intensities``
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200 Phosphopeptide MS intensities where missing values have been **imputed** by the chosen method, in tabular format.
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201
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202 ``imputed_QN_LT_intensities``
0
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203 Phosphopeptide MS intensities where missing values have been **imputed** by the chosen method, quantile-normalized (**QN**), and log10-transformed (**LT**), in tabular format.
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204
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205 ``report_file``
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206 Summary report for normalization, imputation, and **ANOVA**, in PDF format.
0
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207
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208 **Authors**
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209
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210 ``Larry C. Cheng``
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211 (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) wrote the original script.
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212
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213 ``Arthur C. Eschenlauer``
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214 (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy.
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215
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216 ===================================
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217 PERL-compatible regular expressions
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218 ===================================
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219
5
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220 Note that the PERL-compatible regular expressions accepted by this tool are documented at http://rdrr.io/r/base/regex.html
0
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221
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222 ]]></help>
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223 <citations>
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224 <!-- Cheng_2018 "Phosphopeptide Enrichment ..." PMID: 30124664 -->
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225 <citation type="doi">10.3791/57996</citation>
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226 </citations>
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227 </tool>