Mercurial > repos > eschen42 > mqppep_anova
changeset 16:2b9119d7d80a draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7127d1511d45a8b22d4f50eee6db24d844371227"
| author | eschen42 |
|---|---|
| date | Tue, 05 Apr 2022 01:48:08 +0000 |
| parents | 2c5f1a2fe16a |
| children | bb38aac026b9 |
| files | macros.xml mqppep_anova.xml |
| diffstat | 2 files changed, 15 insertions(+), 13 deletions(-) [+] |
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--- a/macros.xml Sat Mar 26 02:27:12 2022 +0000 +++ b/macros.xml Tue Apr 05 01:48:08 2022 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">0.1.6</token> + <token name="@TOOL_VERSION@">0.1.7</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> @@ -13,7 +13,6 @@ <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="1.7.1" >r-optparse</requirement> <requirement type="package" version="2.11" >r-rmarkdown</requirement> <!-- It would be nice to use conda-forge/texlive-core rather than r-tinytex because the
--- a/mqppep_anova.xml Sat Mar 26 02:27:12 2022 +0000 +++ b/mqppep_anova.xml Tue Apr 05 01:48:08 2022 +0000 @@ -1,4 +1,10 @@ -<tool id="mqppep_anova" name="MaxQuant Phosphopeptide ANOVA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5"> +<tool + id="mqppep_anova" + name="MaxQuant Phosphopeptide ANOVA" + version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" + python_template_version="3.5" + profile="21.05" + > <description>Perform ANOVA on merged and filtered data from phospho-peptide enrichment/MaxQuant pipeline</description> <macros> <import>macros.xml</import> @@ -10,16 +16,15 @@ biocontainer are read-only, so this builds a pseudo-home under /tmp --> <command detect_errors="exit_code"><![CDATA[ - export OLD_PWD=\$(dirname \$(pwd)); - export HOME=/tmp\${OLD_PWD}; - mkdir -p \$HOME/bin; - mkdir -p \$HOME/tmp; - export TEMP=\$HOME/tmp; - export TMPDIR=\$TEMP; - cd \$TEMP; + 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; - \${CONDA_PREFIX}/bin/Rscript \$TEMP/mqppep_anova.R + Rscript \${HOME}/mqppep_anova.R --inputFile '$input_file' --alphaFile '$alpha_file' --firstDataColumn $intensity_column_regex_f @@ -34,8 +39,6 @@ --imputedQNLTDataFile '$imp_qn_lt_file' --reportFile '$report_file'; export RESULT=\$?; - cd \${OLD_PWD}; - rm -rf \$HOME; exit \${RESULT} ]]></command> <configfiles>