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annotate monocle3-macros.xml @ 3:6b6b5a6d4021 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 660486ba0e1ef2f0195e7c6f75448221ba4640f7"
author ebi-gxa
date Tue, 28 Apr 2020 11:56:26 -0400
parents 17e74fba97fd
children 8ec85828b6e6
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710d112ee525 "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>
710d112ee525 "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[
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6 **Version history**
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7
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8 0.1.4+galaxy0: Updated to monocle3-cli 0.0.7 to fix bug with column headers in tsv.
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98e99ab36505 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 08ac0ad9182623944c4546f8ea8db6a1a537f7eb
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10 0.1.3+galaxy0: Updated to monocle3-cli 0.0.5 to fix bug with tsv inputs.
98e99ab36505 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 08ac0ad9182623944c4546f8ea8db6a1a537f7eb
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11
0
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12 0.1.2+galaxy0: Initial version based on monocle3-cli 0.0.3 and monocle3 0.1.2
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13 ]]></token>
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14 <token name="@INPUT_OPTS@">
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15 --input-object-format '${input_object_format}' '${input_object_file}'
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16 </token>
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17 <token name="@OUTPUT_OPTS@">
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18 --output-object-format '${output_object_format}' output.RDS
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19 #if $introspective
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20 --introspective
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21 #end if
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22 </token>
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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23 <token name="@VERBOSE@">
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24 #if $verbose
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25 --verbose
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26 #end if
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27 </token>
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28
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29 <xml name="requirements">
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30 <requirements>
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31 <requirement type="package" version="0.0.7">monocle3-cli</requirement>
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32 <yield/>
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33 </requirements>
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34 </xml>
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35
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36 <xml name="citations">
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37 <citations>
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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38 <yield />
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39 <citation type="doi">10.1038/nmeth.4402</citation>
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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40 <citation type="bibtex">
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41 @misc{githubscanpy-scripts,
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42 author = {Ni Huang, Krzysztof Polanski, EBI Gene Expression Team},
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43 year = {2019},
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44 title = {Monocle3-cli: command line interface for Monocle3},
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45 publisher = {GitHub},
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46 journal = {GitHub repository},
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47 url = {https://github.com/ebi-gene-expression-group/monocle-scripts},
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48 }</citation>
3
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49 <citation type="doi">10.1101/2020.04.08.032698</citation>
0
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50 </citations>
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51 </xml>
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52
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53 <xml name="input_object_params">
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54 <param name="input_object_file" argument="input-object-file" type="data" format="rdata" label="Input object in RDS format"/>
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55 <param name="input_object_format" argument="--input-object-format" type="select" label="Format of input object">
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56 <option value="cds3" selected="true">Monocle3 object in RDS</option>
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57 </param>
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58 </xml>
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59
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60 <xml name="output_object_params">
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61 <param name="output_object_format" argument="--output-object-format" type="select" label="Format of output object">
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62 <option value="cds3" selected="true">Monocle3 object in RDS</option>
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63 </param>
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64 <param name="introspective" argument="--introspective" type="boolean" checked="true" label="Print introspective information of output object"/>
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65 </xml>
1
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66
0
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67 <xml name="verbose_flag">
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68 <param name="verbose" argument="--verbose" type="boolean" checked="false" label="Emit verbose output"/>
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69 </xml>
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70 </macros>