Mercurial > repos > ebi-gxa > droplet_barcode_plot
changeset 1:0e985680e67d draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml commit bf9021c853da640771202920cde38f77cdeaf368"
| author | ebi-gxa |
|---|---|
| date | Wed, 04 Mar 2020 06:44:10 -0500 |
| parents | 04f32429dcf2 |
| children | 7782648d8b56 |
| files | dropletBarcodePlot.xml |
| diffstat | 1 files changed, 10 insertions(+), 10 deletions(-) [+] |
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--- a/dropletBarcodePlot.xml Fri Nov 08 09:08:14 2019 -0500 +++ b/dropletBarcodePlot.xml Wed Mar 04 06:44:10 2020 -0500 @@ -1,13 +1,13 @@ -<tool id="_dropletBarcodePlot" name="Droplet barcode rank plot" version="1.6.1+galaxy0"> +<tool id="_dropletBarcodePlot" name="Droplet barcode rank plot" version="1.6.1+galaxy1" profile="18.01"> <description>Creates a barcode rank plot for quality control of droplet single-cell RNA-seq data</description> <requirements> <requirement type="package" version="1.6.1">bioconductor-dropletutils</requirement> - <requirement type="package">openblas</requirement> - <requirement type="package">r-matrix</requirement> - <requirement type="package">r-ggplot2</requirement> - <requirement type="package">r-optparse</requirement> - <requirement type="package">r-gridextra</requirement> - <requirement type="package">bioconductor-delayedarray</requirement> + <requirement type="package" version="0.3.9">openblas</requirement> + <requirement type="package" version="1.2">r-matrix</requirement> + <requirement type="package" version="3.2.1">r-ggplot2</requirement> + <requirement type="package" version="1.6.4">r-optparse</requirement> + <requirement type="package" version="2.3">r-gridextra</requirement> + <requirement type="package" version="0.12.0">bioconductor-delayedarray</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ $__tool_directory__/dropletBarcodePlot.R --output-plot "${plot_file}" --output-thresholds "${thresholds_file}" --label "${label}" --density-bins "${density_bins}" --roryk-multiplier "${roryk_multiplier}" @@ -42,13 +42,13 @@ <data name="plot_file" format="png" label="${tool.name} on ${on_string}: barcode rank plot"/> <data name="thresholds_file" format="txt" label="${tool.name} on ${on_string}: barcode thresholds"/> </outputs> - + <tests> <test> <conditional name='input'> <param name="type" value="barcode_freqs"/> <param name="barcode_frequencies" ftype="txt" value="raw_cb_frequency.txt"/> - </conditional> + </conditional> <output name="plot_file" file="barcode_plot.png"/> </test> </tests> @@ -58,7 +58,7 @@ **What it does** -Given a barcode freqeuncy table or an MTX-format matrix from which one can be calculated, produces a barcode rank plot to assess distinctness of droplets with cells over those without (a key mark of good-quality droplet single-cell RNA-seq data). +Given a barcode freqeuncy table or an MTX-format matrix from which one can be calculated, produces a barcode rank plot to assess distinctness of droplets with cells over those without (a key mark of good-quality droplet single-cell RNA-seq data). Thresholds are calculated and plotted, either with DropletUtils or by custom method discussed at https://github.com/COMBINE-lab/salmon/issues/362#issuecomment-490160480.