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comparison mqppep_anova.xml @ 7:d728198f1ba5 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
author eschen42
date Tue, 15 Mar 2022 00:35:16 +0000
parents d4d531006735
children 4deacfee76ef
comparison
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6:922d309640db 7:d728198f1ba5
1 <tool id="mqppep_anova" name="MaxQuant Phosphopeptide ANOVA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5"> 1 <tool id="mqppep_anova" name="MaxQuant Phosphopeptide ANOVA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
2 <description>Perform ANOVA on merged and filtered data from phospho-peptide enrichment/MaxQuant pipeline</description> 2 <description>Perform ANOVA on merged and filtered data from phospho-peptide enrichment/MaxQuant pipeline</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <expand macro="requirements"/>
7 <requirement type="package" version="1.7.1" >r-optparse</requirement> 7 <!--
8 <requirement type="package" version="1.4.0" >r-stringr</requirement> 8 The weird invocation used here is because knitr and install_tinytex
9 <requirement type="package" version="1.14.2" >r-data.table</requirement> 9 both need access to a writeable directory, but most directories in a
10 <requirement type="package" version="3.3.5" >r-ggplot2</requirement> 10 biocontainer are read-only, so this builds a pseudo-home under /tmp
11 <requirement type="package" version="1.56.0" >bioconductor-preprocesscore</requirement> 11 -->
12 <requirement type="package" version="0.3.3" >openblas</requirement>
13 <requirement type="package" version="2.11" >r-rmarkdown</requirement>
14 <requirement type="package" version="0.4.0" >r-sass</requirement>
15 <requirement type="package" version="20210325">texlive-core</requirement>
16
17 </requirements>
18 <!-- Rscript -e 'rmarkdown::render("QuantDataProcessingScript.Rmd")' -->
19 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
20 cd /tmp; 13 export OLD_PWD=\$(dirname \$(pwd));
14 export HOME=/tmp\${OLD_PWD};
15 mkdir -p \$HOME/bin;
16 mkdir -p \$HOME/tmp;
17 export TEMP=\$HOME/tmp;
18 export TMPDIR=\$TEMP;
19 cd \$TEMP;
21 cp '$__tool_directory__/mqppep_anova_script.Rmd' . || exit 0; 20 cp '$__tool_directory__/mqppep_anova_script.Rmd' . || exit 0;
22 cp '$__tool_directory__/mqppep_anova.R' . || exit 0; 21 cp '$__tool_directory__/mqppep_anova.R' . || exit 0;
23 \${CONDA_PREFIX}/bin/Rscript /tmp/mqppep_anova.R 22 \${CONDA_PREFIX}/bin/Rscript \$TEMP/mqppep_anova.R
24 --inputFile '$input_file' 23 --inputFile '$input_file'
25 --alphaFile $alpha_file 24 --alphaFile $alpha_file
26 --firstDataColumn $first_data_column 25 --firstDataColumn $first_data_column
27 --imputationMethod $imputation.imputation_method 26 --imputationMethod $imputation.imputation_method
28 #if '$imputation_method' == 'random': 27 #if '$imputation_method' == 'random':
31 #end if 30 #end if
32 --regexSampleNames $sample_names_regex_f 31 --regexSampleNames $sample_names_regex_f
33 --regexSampleGrouping $sample_grouping_regex_f 32 --regexSampleGrouping $sample_grouping_regex_f
34 --imputedDataFile $imputed_data_file 33 --imputedDataFile $imputed_data_file
35 --reportFile $report_file; 34 --reportFile $report_file;
36 rm mqppep_anova_script.Rmd; 35 cd \${OLD_PWD};
37 rm mqppep_anova.R 36 rm -rf \$HOME
38 ]]></command> 37 ]]></command>
39 <configfiles> 38 <configfiles>
40 <configfile name="sample_names_regex_f"> 39 <configfile name="sample_names_regex_f">
41 $sample_names_regex 40 $sample_names_regex
42 </configfile> 41 </configfile>
97 </valid> 96 </valid>
98 </sanitizer> 97 </sanitizer>
99 </param> 98 </param>
100 </inputs> 99 </inputs>
101 <outputs> 100 <outputs>
102 <data name="imputed_data_file" format="tabular" label="${input_file.name}.intensities_${imputation.imputation_method}-imputed_QN_LT" ></data> 101 <data name="imputed_data_file" format="tabular" label="${input_file.name}.${imputation.imputation_method}-imputed_QN_LT_intensities" ></data>
103 <data name="report_file" format="html" label="${input_file.name}.report (download/unzip to view)" ></data> 102 <!--
103 <data name="report_file" format="html" label="${input_file.name}.${imputation.imputation_method}-imputed_report (download/unzip to view)" ></data>
104 -->
105 <data name="report_file" format="pdf" label="${input_file.name}.${imputation.imputation_method}-imputed_report" ></data>
104 </outputs> 106 </outputs>
105 <tests> 107 <tests>
106 <test> 108 <test>
107 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/> 109 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
108 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/> 110 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
122 <test> 124 <test>
123 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/> 125 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
124 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/> 126 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
125 <param name="first_data_column" value="10"/> 127 <param name="first_data_column" value="10"/>
126 <param name="imputation_method" value="random"/> 128 <param name="imputation_method" value="random"/>
129 <param name="meanPercentile" value="1" />
130 <param name="sdPercentile" value="0.2" />
127 <param name="sample_names_regex" value="\.\d+[A-Z]$"/> 131 <param name="sample_names_regex" value="\.\d+[A-Z]$"/>
128 <param name="sample_grouping_regex" value="\d+"/> 132 <param name="sample_grouping_regex" value="\d+"/>
129 <output name="imputed_data_file"> 133 <output name="imputed_data_file">
130 <assert_contents> 134 <assert_contents>
131 <has_text text="Phosphopeptide" /> 135 <has_text text="Phosphopeptide" />
190 194
191 ``intensities_*-imputed_QN_LT`` 195 ``intensities_*-imputed_QN_LT``
192 Phosphopeptide MS intensities where missing values have been **imputed** by the chosen method, quantile-normalized (**QN**), and log10-transformed (**LT**), in tabular format. 196 Phosphopeptide MS intensities where missing values have been **imputed** by the chosen method, quantile-normalized (**QN**), and log10-transformed (**LT**), in tabular format.
193 197
194 ``report_file`` 198 ``report_file``
195 (download/unzip to view) Summary report for normalization, imputation, and ANOVA. 199 Summary report for normalization, imputation, and ANOVA, in PDF format.
196 This dataset is displayed in Galaxy as having a datatype of ``html`` in Galaxy,
197 but it is in fact a zipfile; the zip file contains
198 an HTML file. Please download and unzip it locally to view the report.
199 Ideally this report would be a PDF, but there is an issue
200 `(linked here)
201 <https://github.com/conda-forge/texlive-core-feedstock/issues/19>`_.
202 that needs to be resolved first.
203 200
204 **Authors** 201 **Authors**
205 202
206 ``Larry C. Cheng`` 203 ``Larry C. Cheng``
207 (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) wrote the original script. 204 (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) wrote the original script.