Mercurial > repos > eschen42 > mqppep_anova
changeset 17:bb38aac026b9 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit aea9ac5a98069c3c993bd7903eda732f8ae2109d"
| author | eschen42 |
|---|---|
| date | Wed, 06 Apr 2022 05:48:05 +0000 |
| parents | 2b9119d7d80a |
| children | e6a81acd1eb2 |
| files | macros.xml mqppep_anova.xml |
| diffstat | 2 files changed, 15 insertions(+), 21 deletions(-) [+] |
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--- a/macros.xml Tue Apr 05 01:48:08 2022 +0000 +++ b/macros.xml Wed Apr 06 05:48:05 2022 +0000 @@ -1,19 +1,17 @@ <macros> - <token name="@TOOL_VERSION@">0.1.7</token> + <token name="@TOOL_VERSION@">0.1.8</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="0.3.3" >openblas</requirement> <requirement type="package" version="0.4.0" >r-sass</requirement> <requirement type="package" version="1.14.2" >r-data.table</requirement> + <requirement type="package" version="1.56.0" >bioconductor-preprocesscore</requirement> + <requirement type="package" version="5.26.2" >perl</requirement> + <requirement type="package" version="0.3.3" >openblas</requirement> <requirement type="package" version="1.22.2" >numpy</requirement> - <requirement type="package" version="1.4.0" >pyahocorasick</requirement> - <requirement type="package" version="1.4.0" >r-stringr</requirement> - <requirement type="package" version="1.4.1" >pandas</requirement> - <requirement type="package" version="1.56.0" >bioconductor-preprocesscore</requirement> - <requirement type="package" version="1.64" >perl-dbd-sqlite</requirement> - <requirement type="package" version="1.7.1" >r-optparse</requirement> - <requirement type="package" version="2.11" >r-rmarkdown</requirement> + <requirement type="package" version="3.3.5" >r-ggplot2</requirement> + <requirement type="package" version="0.3.7" >r-vioplot</requirement> + <requirement type="package" version="0.37" >r-tinytex</requirement> <!-- It would be nice to use conda-forge/texlive-core rather than r-tinytex because the former installs texlive when the package is built, but issue 23 blocked PDF-creation. @@ -21,12 +19,14 @@ with boxes) unless I specified the build as well as the version when building a conda environment, e.g.: texlive-core=20210325=h97429d4_0 --> - <requirement type="package" version="0.37" >r-tinytex</requirement> - <requirement type="package" version="3.3.5" >r-ggplot2</requirement> <requirement type="package" version="3.9.10" >python</requirement> - <requirement type="package" version="5.26.2" >perl</requirement> <requirement type="package" version="0.9.4" >r-latex2exp</requirement> - <requirement type="package" version="0.3.7" >r-vioplot</requirement> + <requirement type="package" version="1.4.0" >r-stringr</requirement> + <requirement type="package" version="1.64" >perl-dbd-sqlite</requirement> + <requirement type="package" version="1.4.0" >pyahocorasick</requirement> + <requirement type="package" version="2.11" >r-rmarkdown</requirement> + <requirement type="package" version="1.4.1" >pandas</requirement> + <requirement type="package" version="1.7.1" >r-optparse</requirement> </requirements> </xml> </macros>
--- a/mqppep_anova.xml Tue Apr 05 01:48:08 2022 +0000 +++ b/mqppep_anova.xml Wed Apr 06 05:48:05 2022 +0000 @@ -16,15 +16,9 @@ biocontainer are read-only, so this builds a pseudo-home under /tmp --> <command detect_errors="exit_code"><![CDATA[ - export HOME=\${_GALAXY_JOB_HOME_DIR}; - export TEMP=\${_GALAXY_JOB_TMP_DIR}; - export TMPDIR=\${TEMP}; - mkdir -p \${HOME}/bin; - mkdir -p \${HOME}/tmp; - cd \${HOME}; cp '$__tool_directory__/mqppep_anova_script.Rmd' . || exit 0; - cp '$__tool_directory__/mqppep_anova.R' . || exit 0; - Rscript \${HOME}/mqppep_anova.R + cp '$__tool_directory__/mqppep_anova.R' . || exit 0; + Rscript mqppep_anova.R --inputFile '$input_file' --alphaFile '$alpha_file' --firstDataColumn $intensity_column_regex_f