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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml commit 39412ddc5dbeb136161a9d9fb0f9f78520159ccc"
author | ebi-gxa |
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date | Tue, 24 Mar 2020 12:03:14 -0400 |
parents | 7782648d8b56 |
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<tool id="_dropletBarcodePlot" name="Droplet barcode rank plot" version="1.6.1+galaxy2" 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="0.0.1">scxa-plots</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ dropletBarcodePlot.R --output-plot "${plot_file}" --output-thresholds "${thresholds_file}" --label "${label}" --density-bins "${density_bins}" --roryk-multiplier "${roryk_multiplier}" #if $input.type == 'mtx_matrix' --mtx-matrix ${input.mtx_matrix} #if $input.cellsbyrow --cells-by-row #end if #end if #if $input.type == 'barcode_freqs' --barcode-frequencies ${input.barcode_frequencies} #end if ]]></command> <inputs> <conditional name="input"> <param name="type" type="boolean" truevalue='mtx_matrix' falsevalue='barcode_freqs' checked="true" label="Input MTX-format matrix?" help="Barcode frequencies will be calculated for you. The alternative is to provide barcode frequencies directly"/> <when value="mtx_matrix"> <param name="mtx_matrix" type="data" format="mtx" label="Matrix-market format matrix file, with cells by column (overrides --barcode-frequencies if supplied)" /> <param name="cellsbyrow" type="boolean" checked="false" label="For use with --mtx-matrix: force interpretation of matrix to assume cells are by row, rather than by column (default)"/> </when> <when value="barcode_freqs"> <param name="barcode_frequencies" type="data" format="txt" label="A two-column tab-delimited file, with barcodes in the first column and frequencies in the second" /> </when> </conditional> <param name="label" type="text" optional='true' value="" label="Label to place in plot title"/> <param name="density_bins" type="integer" value="50" label="Number of bins used in barcode count frequency distribution"/> <param name="roryk_multiplier" type="float" value="1.5" label="Above-baseline multiplier to calculate roryk threshold"/> </inputs> <outputs> <data name="plot_file" format="png" label="${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> <output name="plot_file" file="barcode_plot.png"/> </test> </tests> <help><![CDATA[ .. class:: infomark **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). Thresholds are calculated and plotted, either with DropletUtils or by custom method discussed at https://github.com/COMBINE-lab/salmon/issues/362#issuecomment-490160480. **Inputs** * two-column tab-delimted text file with barcode frequencies OR an MTX-format matrix file ----- **Outputs** * PNG-format plot file. ]]></help> <citations> <citation type="bibtex"> @misc{github-hinxton-single-cell, author = {Jonathan Manning, EBI Gene Expression Team}, year = {2019}, title = {Hinxton Single Cell Anlysis Environment}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary}, }</citation> </citations> </tool>