Mercurial > repos > ebi-gxa > monocle3_topmarkers

annotate monocle3-macros.xml @ 0:bc2df96ef963 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
author ebi-gxa
date Thu, 14 May 2020 17:17:27 -0400
parents
children a4ab4af54b1a
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bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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1 <macros>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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2 <token name="@TOOL_VERSION@">0.1.4</token>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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3 <token name="@PROFILE@">18.01</token>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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4 <token name="@HELP@">More information can be found at https://cole-trapnell-lab.github.io/monocle3/ and https://github.com/ebi-gene-expression-group/monocle-scripts</token>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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5 <token name="@VERSION_HISTORY@"><![CDATA[
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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6 **Version history**
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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7 0.1.5+galaxy0: Updated to monocle3-cli 0.0.8 to add top marker genes and fix container plots for plotCells (only those two modules upgraded).
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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8
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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9 0.1.4+galaxy0: Updated to monocle3-cli 0.0.7 to fix bug with column headers in tsv.
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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10
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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11 0.1.3+galaxy0: Updated to monocle3-cli 0.0.5 to fix bug with tsv inputs.
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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12
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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13 0.1.2+galaxy0: Initial version based on monocle3-cli 0.0.3 and monocle3 0.1.2
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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14 ]]></token>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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15 <token name="@INPUT_OPTS@">
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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16 --input-object-format '${input_object_format}' '${input_object_file}'
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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17 </token>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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18 <token name="@OUTPUT_OPTS@">
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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19 --output-object-format '${output_object_format}' output.RDS
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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20 #if $introspective
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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21 --introspective
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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22 #end if
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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23 </token>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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24 <token name="@VERBOSE@">
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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25 #if $verbose
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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26 --verbose
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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27 #end if
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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28 </token>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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29
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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30 <xml name="requirements">
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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31 <requirements>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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32 <requirement type="package" version="0.0.7">monocle3-cli</requirement>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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33 <yield/>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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34 </requirements>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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35 </xml>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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36
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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37 <xml name="citations">
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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38 <citations>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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39 <yield />
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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40 <citation type="doi">10.1038/nmeth.4402</citation>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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41 <citation type="bibtex">
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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42 @misc{githubscanpy-scripts,
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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43 author = {Ni Huang, Krzysztof Polanski, EBI Gene Expression Team},
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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44 year = {2019},
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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45 title = {Monocle3-cli: command line interface for Monocle3},
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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46 publisher = {GitHub},
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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47 journal = {GitHub repository},
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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48 url = {https://github.com/ebi-gene-expression-group/monocle-scripts},
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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49 }</citation>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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50 <citation type="doi">10.1101/2020.04.08.032698</citation>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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51 </citations>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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52 </xml>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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53
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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54 <xml name="input_object_params">
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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55 <param name="input_object_file" argument="input-object-file" type="data" format="rdata" label="Input object in RDS format"/>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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56 <param name="input_object_format" argument="--input-object-format" type="select" label="Format of input object">
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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57 <option value="cds3" selected="true">Monocle3 object in RDS</option>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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58 </param>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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59 </xml>
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60
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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61 <xml name="output_object_params">
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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62 <param name="output_object_format" argument="--output-object-format" type="select" label="Format of output object">
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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63 <option value="cds3" selected="true">Monocle3 object in RDS</option>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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64 </param>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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65 <param name="introspective" argument="--introspective" type="boolean" checked="true" label="Print introspective information of output object"/>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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66 </xml>
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67
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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68 <xml name="verbose_flag">
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69 <param name="verbose" argument="--verbose" type="boolean" checked="false" label="Emit verbose output"/>
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70 </xml>
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71 </macros>