Mercurial > repos > ebi-gxa > scanpy_run_paga

annotate scanpy_macros2.xml @ 0:3e53344e540d draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
author ebi-gxa
date Mon, 16 Sep 2019 08:25:36 -0400
parents
children 77bc9501765d
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3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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1 <macros>
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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2 <token name="@TOOL_VERSION@">1.4.2</token>
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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3 <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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4 <token name="@VERSION_HISTORY@"><![CDATA[
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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5 **Version history**
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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6
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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7 1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2).
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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8
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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9 1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files.
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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10
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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11 1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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12 EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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13 ]]></token>
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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14 <token name="@INPUT_OPTS@">
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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15 --input-format '${input_format}' input.h5
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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16 </token>
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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17 <token name="@OUTPUT_OPTS@">
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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18 --show-obj stdout --output-format '${output_format}' output.h5
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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19 </token>
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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20 <token name="@PLOT_OPTS@">
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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21 #if $fig_title
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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22 --title '${fig_title}'
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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23 #end if
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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24 --fig-size '${fig_size}'
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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25 --fig-dpi ${fig_dpi}
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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26 --fig-fontsize ${fig_fontsize}
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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27 ${fig_frame}
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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28 ./output.png
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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29 </token>
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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30 <token name="@EXPORT_MTX_OPTS@">${export_mtx}</token>
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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31
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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32 <xml name="requirements">
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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33 <requirements>
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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34 <requirement type="package" version="0.2.4.post4">scanpy-scripts</requirement>
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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35 <yield/>
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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36 </requirements>
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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37 </xml>
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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38
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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39 <xml name="citations">
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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40 <citations>
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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41 <yield />
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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42 <citation type="doi">10.1186/s13059-017-1382-0</citation>
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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43 <citation type="bibtex">
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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44 @misc{githubscanpy-scripts,
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45 author = {Ni Huang, EBI Gene Expression Team},
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46 year = {2018},
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47 title = {Scanpy-scripts: command line interface for Scanpy},
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48 publisher = {GitHub},
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49 journal = {GitHub repository},
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50 url = {https://github.com/ebi-gene-expression-group/scanpy-scripts},
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51 }</citation>
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52 </citations>
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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53 </xml>
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54
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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55 <xml name="input_object_params">
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56 <param name="input_obj_file" argument="input-object-file" type="data" format="h5" label="Input object in hdf5 format"/>
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57 <param name="input_format" argument="--input-format" type="select" label="Format of input object">
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58 <option value="anndata" selected="true">AnnData format hdf5</option>
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59 <option value="loom">Loom format hdf5</option>
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60 </param>
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61 </xml>
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62
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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63 <xml name="output_object_params">
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64 <param name="output_format" argument="--output-format" type="select" label="Format of output object">
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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65 <option value="anndata" selected="true">AnnData format hdf5</option>
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66 <option value="loom">Loom format hdf5</option>
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67 </param>
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68 </xml>
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69
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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70 <xml name="output_plot_params">
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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71 <param name="fig_title" argument="--title" type="text" label="Figure title"/>
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72 <param name="fig_size" argument="--fig-size" type="text" value="4,4" label="Figure size as 'width,height', e.g, '7,7'"/>
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73 <param name="fig_dpi" argument="--fig-dpi" type="integer" min="1" value="80" label="Figure dpi"/>
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74 <param name="fig_fontsize" argument="--fig-fontsize" type="integer" min="0" value="10" label="Figure font size"/>
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75 <param name="fig_frame" type="boolean" truevalue="--frameon" falsevalue="--frameoff" checked="false"
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76 label="Show plot frame"/>
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77 </xml>
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78
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79 <xml name="export_mtx_params">
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80 <param name="export_mtx" argument="--export-mtx" type="boolean" truevalue="--export-mtx ./" falsevalue="" checked="false" label="Save normalised data to 10x mtx format" help="If enabled, it will generate in addition to the main output in Loom or AnnData an export in 10x format of the normalised data."/>
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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81 </xml>
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82
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83 <xml name="export_mtx_outputs">
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84 <data name="matrix_10x" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: 10x matrix">
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85 <filter>export_mtx</filter>
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86 </data>
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87 <data name="genes_10x" format="tsv" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: 10x genes">
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88 <filter>export_mtx</filter>
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89 </data>
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90 <data name="barcodes_10x" format="tsv" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: 10x barcodes">
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91 <filter>export_mtx</filter>
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92 </data>
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93 </xml>
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94 </macros>