Mercurial > repos > eschen42 > mqppep_anova
diff mqppep_anova.xml @ 5:d4d531006735 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
| author | eschen42 |
|---|---|
| date | Thu, 10 Mar 2022 23:42:48 +0000 |
| parents | c1403d18c189 |
| children | d728198f1ba5 |
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--- a/mqppep_anova.xml Mon Mar 07 20:43:57 2022 +0000 +++ b/mqppep_anova.xml Thu Mar 10 23:42:48 2022 +0000 @@ -4,33 +4,37 @@ <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="1.7.1">r-optparse</requirement> - <requirement type="package" version="1.4.0">r-stringr</requirement> - <requirement type="package" version="1.14.2">r-data.table</requirement> - <requirement type="package" version="3.3.5">r-ggplot2</requirement> - <requirement type="package" version="1.56.0">bioconductor-preprocesscore</requirement> - <requirement type="package" version="0.3.3" >openblas</requirement> - <requirement type="package" version="2.11" >r-rmarkdown</requirement> - <requirement type="package" version="0.4.0" >r-sass</requirement> - <requirement type="package" >texlive-core</requirement> + <requirement type="package" version="1.7.1" >r-optparse</requirement> + <requirement type="package" version="1.4.0" >r-stringr</requirement> + <requirement type="package" version="1.14.2" >r-data.table</requirement> + <requirement type="package" version="3.3.5" >r-ggplot2</requirement> + <requirement type="package" version="1.56.0" >bioconductor-preprocesscore</requirement> + <requirement type="package" version="0.3.3" >openblas</requirement> + <requirement type="package" version="2.11" >r-rmarkdown</requirement> + <requirement type="package" version="0.4.0" >r-sass</requirement> + <requirement type="package" version="20210325">texlive-core</requirement> </requirements> <!-- Rscript -e 'rmarkdown::render("QuantDataProcessingScript.Rmd")' --> <command detect_errors="exit_code"><![CDATA[ -cat $sample_names_regex_f; cat $sample_grouping_regex_f; -Rscript '$__tool_directory__/mqppep_anova.R' ---inputFile '$input_file' ---alphaFile $alpha_file ---firstDataColumn $first_data_column ---imputationMethod $imputation.imputation_method -#if '$imputation_method' == 'random': - --meanPercentile '$meanPercentile' - --sdPercentile '$sdPercentile' -#end if ---regexSampleNames $sample_names_regex_f ---regexSampleGrouping $sample_grouping_regex_f ---imputedDataFile $imputed_data_file ---reportFile $report_file + cd /tmp; + cp '$__tool_directory__/mqppep_anova_script.Rmd' . || exit 0; + cp '$__tool_directory__/mqppep_anova.R' . || exit 0; + \${CONDA_PREFIX}/bin/Rscript /tmp/mqppep_anova.R + --inputFile '$input_file' + --alphaFile $alpha_file + --firstDataColumn $first_data_column + --imputationMethod $imputation.imputation_method + #if '$imputation_method' == 'random': + --meanPercentile '$meanPercentile' + --sdPercentile '$sdPercentile' + #end if + --regexSampleNames $sample_names_regex_f + --regexSampleGrouping $sample_grouping_regex_f + --imputedDataFile $imputed_data_file + --reportFile $report_file; + rm mqppep_anova_script.Rmd; + rm mqppep_anova.R ]]></command> <configfiles> <configfile name="sample_names_regex_f"> @@ -109,9 +113,9 @@ <output name="imputed_data_file"> <assert_contents> <has_text text="Phosphopeptide" /> - <has_text text="AAAAAAAGDpSDpSWDADAFSVEDPVRK" /> - <has_text text="23574000" /> - <has_text text="pSESELIDELSEDFDR" /> + <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" /> + <has_text text="7.935878" /> + <has_text text="pSQKQEEENPAEETGEEK" /> </assert_contents> </output> </test> @@ -125,9 +129,9 @@ <output name="imputed_data_file"> <assert_contents> <has_text text="Phosphopeptide" /> - <has_text text="AAAAAAAGDpSDpSWDADAFSVEDPVRK" /> - <has_text text="997800000" /> - <has_text text="pSESELIDELSEDFDR" /> + <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" /> + <has_text text="0.82258" /> + <has_text text="pSQKQEEENPAEETGEEK" /> </assert_contents> </output> </test> @@ -209,7 +213,7 @@ PERL-compatible regular expressions =================================== -Note that the PERL-compatible regular expressions accepted by this tool are documented at https://rdrr.io/r/base/regex.html +Note that the PERL-compatible regular expressions accepted by this tool are documented at http://rdrr.io/r/base/regex.html ]]></help> <citations>