Mercurial > repos > qfabrepo > metadegalaxy_phyloseq_richness
view phyloseq_richness.xml @ 0:0ab4501d805b draft
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
author | qfabrepo |
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date | Mon, 14 Sep 2020 07:38:57 +0000 |
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children | e0225f3e8ef6 |
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<tool id="phyloseq_richness" name="Phyloseq Richness" version="1.22.3.2" hidden="false"> <description>Phyloseq Richness Plot</description> <requirements> <requirement type="package" version="1.22.3">bioconductor-phyloseq</requirement> <requirement type="package" version="1.20.0">r-getopt</requirement> <requirement type="package" version="9.18">ghostscript</requirement> </requirements> <version_command><![CDATA[ echo $(R --version | grep version | grep -v GNU)", phyloseq version" $(R --vanilla --slave -e "library(phyloseq); cat(sessionInfo()\$otherPkgs\$phyloseq\$Version)" 2> /dev/null | grep -v -i "WARNING: ") ]]></version_command> <command detect_errors="exit_code"><![CDATA[ Rscript '${__tool_directory__}/phyloseq_richness.r' --biomfile='$biom_input' --metafile='$metadata_input' --xcolumn="${xaxis_column}" --lcolumn="${legend_column}" --outdir="$htmlfile.files_path" --htmlfile='$htmlfile' ]]></command> <inputs> <param format="biom1" name="biom_input" type="data" label="BIOM file"/> <param format="tabular" name="metadata_input" type="data" label="Metadata file"/> <param name="xaxis_column" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used for X-axis"/> <param name="legend_column" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used as legend"/> </inputs> <outputs> <data format="html" name="htmlfile" label="${tool.name}.html"/> </outputs> <tests> <test> <param name="biom_input" value="test.biom" ftype="biom1" /> <param name="metadata_input" value="metadata.txt" /> <param name="xaxis_column" value="5" /> <param name="legend_column" value="4" /> <output name="htmlfile" ftype="html" file="biom_out.html" /> </test> </tests> <help> **What it does** Creates an alpha biodivesrsity abundance plot using an R package called phyloseq_. .. _phyloseq: https://joey711.github.io/phyloseq/plot_richness-examples.html ----- **Input** - **BIOM file** - this is a BIOM_ file format - **Metadata file** - this is a metadata file of the experiment design - **Column used for X-axis** - The horizontal x-axis display on the barplot. - **Column used as legend** - select a group from the metadata to fill color to represent the group it belongs to. .. _BIOM: http://biom-format.org/ ----- ========= Resources ========= **Wrapper Authors** QFAB Bioinformatics (support@qfab.org) </help> <citations> <citation type="doi">10.18129/B9.bioc.phyloseq</citation> <citation type="doi">doi:10.1186/2047-217X-1-7</citation> </citations> ----- </help> </tool>