Mercurial > repos > ebi-gxa > droplet_barcode_plot

comparison dropletBarcodePlot.xml @ 1:0e985680e67d draft

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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 bf9021c853da640771202920cde38f77cdeaf368"
author ebi-gxa
date Wed, 04 Mar 2020 06:44:10 -0500
parents 04f32429dcf2
children 7782648d8b56
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0:04f32429dcf2 1:0e985680e67d
1 <tool id="_dropletBarcodePlot" name="Droplet barcode rank plot" version="1.6.1+galaxy0"> 1 <tool id="_dropletBarcodePlot" name="Droplet barcode rank plot" version="1.6.1+galaxy1" profile="18.01">
2 <description>Creates a barcode rank plot for quality control of droplet single-cell RNA-seq data</description> 2 <description>Creates a barcode rank plot for quality control of droplet single-cell RNA-seq data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.6.1">bioconductor-dropletutils</requirement> 4 <requirement type="package" version="1.6.1">bioconductor-dropletutils</requirement>
5 <requirement type="package">openblas</requirement> 5 <requirement type="package" version="0.3.9">openblas</requirement>
6 <requirement type="package">r-matrix</requirement> 6 <requirement type="package" version="1.2">r-matrix</requirement>
7 <requirement type="package">r-ggplot2</requirement> 7 <requirement type="package" version="3.2.1">r-ggplot2</requirement>
8 <requirement type="package">r-optparse</requirement> 8 <requirement type="package" version="1.6.4">r-optparse</requirement>
9 <requirement type="package">r-gridextra</requirement> 9 <requirement type="package" version="2.3">r-gridextra</requirement>
10 <requirement type="package">bioconductor-delayedarray</requirement> 10 <requirement type="package" version="0.12.0">bioconductor-delayedarray</requirement>
11 </requirements> 11 </requirements>
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 $__tool_directory__/dropletBarcodePlot.R --output-plot "${plot_file}" --output-thresholds "${thresholds_file}" --label "${label}" --density-bins "${density_bins}" --roryk-multiplier "${roryk_multiplier}" 13 $__tool_directory__/dropletBarcodePlot.R --output-plot "${plot_file}" --output-thresholds "${thresholds_file}" --label "${label}" --density-bins "${density_bins}" --roryk-multiplier "${roryk_multiplier}"
14 #if $input.type == 'mtx_matrix' 14 #if $input.type == 'mtx_matrix'
15 --mtx-matrix ${input.mtx_matrix} 15 --mtx-matrix ${input.mtx_matrix}
40 40
41 <outputs> 41 <outputs>
42 <data name="plot_file" format="png" label="${tool.name} on ${on_string}: barcode rank plot"/> 42 <data name="plot_file" format="png" label="${tool.name} on ${on_string}: barcode rank plot"/>
43 <data name="thresholds_file" format="txt" label="${tool.name} on ${on_string}: barcode thresholds"/> 43 <data name="thresholds_file" format="txt" label="${tool.name} on ${on_string}: barcode thresholds"/>
44 </outputs> 44 </outputs>
45 45
46 <tests> 46 <tests>
47 <test> 47 <test>
48 <conditional name='input'> 48 <conditional name='input'>
49 <param name="type" value="barcode_freqs"/> 49 <param name="type" value="barcode_freqs"/>
50 <param name="barcode_frequencies" ftype="txt" value="raw_cb_frequency.txt"/> 50 <param name="barcode_frequencies" ftype="txt" value="raw_cb_frequency.txt"/>
51 </conditional> 51 </conditional>
52 <output name="plot_file" file="barcode_plot.png"/> 52 <output name="plot_file" file="barcode_plot.png"/>
53 </test> 53 </test>
54 </tests> 54 </tests>
55 55
56 <help><![CDATA[ 56 <help><![CDATA[
57 .. class:: infomark 57 .. class:: infomark
58 58
59 **What it does** 59 **What it does**
60 60
61 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). 61 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).
62 62
63 Thresholds are calculated and plotted, either with DropletUtils or by custom method discussed at https://github.com/COMBINE-lab/salmon/issues/362#issuecomment-490160480. 63 Thresholds are calculated and plotted, either with DropletUtils or by custom method discussed at https://github.com/COMBINE-lab/salmon/issues/362#issuecomment-490160480.
64 64
65 **Inputs** 65 **Inputs**
66 66