Mercurial > repos > ebi-gxa > droplet_barcode_plot

annotate dropletBarcodePlot.xml @ 3:8f605643ccfd draft default tip

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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
date Tue, 24 Mar 2020 12:03:14 -0400
parents 7782648d8b56
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7782648d8b56 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml commit 6f31a23343fd7d0a834eebe268d820733eb483b5"
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1 <tool id="_dropletBarcodePlot" name="Droplet barcode rank plot" version="1.6.1+galaxy2" profile="18.01">
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2 <description>Creates a barcode rank plot for quality control of droplet single-cell RNA-seq data</description>
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3 <requirements>
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4 <requirement type="package" version="0.0.1">scxa-plots</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 dropletBarcodePlot.R --output-plot "${plot_file}" --output-thresholds "${thresholds_file}" --label "${label}" --density-bins "${density_bins}" --roryk-multiplier "${roryk_multiplier}"
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8 #if $input.type == 'mtx_matrix'
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9 --mtx-matrix ${input.mtx_matrix}
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10 #if $input.cellsbyrow
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11 --cells-by-row
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12 #end if
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13 #end if
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14 #if $input.type == 'barcode_freqs'
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15 --barcode-frequencies ${input.barcode_frequencies}
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16 #end if
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17 ]]></command>
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19 <inputs>
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20 <conditional name="input">
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21 <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"/>
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22 <when value="mtx_matrix">
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23 <param name="mtx_matrix" type="data" format="mtx" label="Matrix-market format matrix file, with cells by column (overrides --barcode-frequencies if supplied)" />
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24 <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)"/>
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25 </when>
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26 <when value="barcode_freqs">
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27 <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" />
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28 </when>
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29 </conditional>
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30 <param name="label" type="text" optional='true' value="" label="Label to place in plot title"/>
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31 <param name="density_bins" type="integer" value="50" label="Number of bins used in barcode count frequency distribution"/>
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32 <param name="roryk_multiplier" type="float" value="1.5" label="Above-baseline multiplier to calculate roryk threshold"/>
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33 </inputs>
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35 <outputs>
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36 <data name="plot_file" format="png" label="${tool.name} on ${on_string}: barcode rank plot"/>
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37 <data name="thresholds_file" format="txt" label="${tool.name} on ${on_string}: barcode thresholds"/>
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38 </outputs>
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39
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40 <tests>
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41 <test>
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42 <conditional name='input'>
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43 <param name="type" value="barcode_freqs"/>
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44 <param name="barcode_frequencies" ftype="txt" value="raw_cb_frequency.txt"/>
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45 </conditional>
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46 <output name="plot_file" file="barcode_plot.png"/>
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47 </test>
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48 </tests>
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49
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50 <help><![CDATA[
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51 .. class:: infomark
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52
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53 **What it does**
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54
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55 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).
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56
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57 Thresholds are calculated and plotted, either with DropletUtils or by custom method discussed at https://github.com/COMBINE-lab/salmon/issues/362#issuecomment-490160480.
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58
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59 **Inputs**
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61 * two-column tab-delimted text file with barcode frequencies OR an MTX-format matrix file
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63 -----
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64
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65 **Outputs**
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67 * PNG-format plot file.
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68 ]]></help>
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69 <citations>
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70 <citation type="bibtex">
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71 @misc{github-hinxton-single-cell,
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72 author = {Jonathan Manning, EBI Gene Expression Team},
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73 year = {2019},
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74 title = {Hinxton Single Cell Anlysis Environment},
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75 publisher = {GitHub},
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76 journal = {GitHub repository},
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77 url = {https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary},
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78 }</citation>
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79 </citations>
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80 </tool>