Mercurial > repos > ebi-gxa > monocle3_partition

annotate monocle3-macros.xml @ 4:b253a59cbb98 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 17:18:54 -0400
parents 60cedaee808d
children d98b4705eb4c
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rev   line source
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be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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1 <macros>
2
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2 <token name="@TOOL_VERSION@">0.1.4</token>
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3 <token name="@PROFILE@">18.01</token>
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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>
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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5 <token name="@VERSION_HISTORY@"><![CDATA[
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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6 **Version history**
4
b253a59cbb98 "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).
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8
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9 0.1.4+galaxy0: Updated to monocle3-cli 0.0.7 to fix bug with column headers in tsv.
92ca41fbc123 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8ef74a1abb7d22b5c18611b8cdd7a5bf56c51b10"
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10
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426e1a869cb3 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 08ac0ad9182623944c4546f8ea8db6a1a537f7eb
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11 0.1.3+galaxy0: Updated to monocle3-cli 0.0.5 to fix bug with tsv inputs.
426e1a869cb3 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 08ac0ad9182623944c4546f8ea8db6a1a537f7eb
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12
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13 0.1.2+galaxy0: Initial version based on monocle3-cli 0.0.3 and monocle3 0.1.2
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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14 ]]></token>
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15 <token name="@INPUT_OPTS@">
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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16 --input-object-format '${input_object_format}' '${input_object_file}'
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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17 </token>
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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18 <token name="@OUTPUT_OPTS@">
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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19 --output-object-format '${output_object_format}' output.RDS
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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20 #if $introspective
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21 --introspective
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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22 #end if
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23 </token>
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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24 <token name="@VERBOSE@">
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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25 #if $verbose
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26 --verbose
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27 #end if
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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28 </token>
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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29
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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30 <xml name="requirements">
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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31 <requirements>
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32 <requirement type="package" version="0.0.7">monocle3-cli</requirement>
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33 <yield/>
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34 </requirements>
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35 </xml>
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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36
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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37 <xml name="citations">
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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38 <citations>
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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39 <yield />
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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40 <citation type="doi">10.1038/nmeth.4402</citation>
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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41 <citation type="bibtex">
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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42 @misc{githubscanpy-scripts,
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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43 author = {Ni Huang, Krzysztof Polanski, EBI Gene Expression Team},
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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44 year = {2019},
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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45 title = {Monocle3-cli: command line interface for Monocle3},
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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46 publisher = {GitHub},
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47 journal = {GitHub repository},
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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48 url = {https://github.com/ebi-gene-expression-group/monocle-scripts},
be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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49 }</citation>
3
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50 <citation type="doi">10.1101/2020.04.08.032698</citation>
0
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51 </citations>
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52 </xml>
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53
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54 <xml name="input_object_params">
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55 <param name="input_object_file" argument="input-object-file" type="data" format="rdata" label="Input object in RDS format"/>
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56 <param name="input_object_format" argument="--input-object-format" type="select" label="Format of input object">
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57 <option value="cds3" selected="true">Monocle3 object in RDS</option>
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58 </param>
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59 </xml>
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60
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61 <xml name="output_object_params">
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62 <param name="output_object_format" argument="--output-object-format" type="select" label="Format of output object">
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63 <option value="cds3" selected="true">Monocle3 object in RDS</option>
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64 </param>
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65 <param name="introspective" argument="--introspective" type="boolean" checked="true" label="Print introspective information of output object"/>
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66 </xml>
1
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67
0
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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>