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annotate monocle3-macros.xml @ 1:98e99ab36505 draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 08ac0ad9182623944c4546f8ea8db6a1a537f7eb
author ebi-gxa
date Wed, 29 Jan 2020 10:38:03 -0500
parents 710d112ee525
children 17e74fba97fd
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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>
1
98e99ab36505 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 08ac0ad9182623944c4546f8ea8db6a1a537f7eb
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2 <token name="@TOOL_VERSION@">0.1.3</token>
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3 <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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4 <token name="@VERSION_HISTORY@"><![CDATA[
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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5 **Version history**
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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6
1
98e99ab36505 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 08ac0ad9182623944c4546f8ea8db6a1a537f7eb
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7 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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8
0
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9 0.1.2+galaxy0: Initial version based on monocle3-cli 0.0.3 and monocle3 0.1.2
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10 ]]></token>
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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11 <token name="@INPUT_OPTS@">
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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12 --input-object-format '${input_object_format}' '${input_object_file}'
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13 </token>
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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14 <token name="@OUTPUT_OPTS@">
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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15 --output-object-format '${output_object_format}' output.RDS
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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16 #if $introspective
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17 --introspective
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18 #end if
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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19 </token>
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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20 <token name="@VERBOSE@">
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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21 #if $verbose
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22 --verbose
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23 #end if
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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24 </token>
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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25
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26 <xml name="requirements">
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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27 <requirements>
1
98e99ab36505 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 08ac0ad9182623944c4546f8ea8db6a1a537f7eb
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28 <requirement type="package" version="0.0.5">monocle3-cli</requirement>
0
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29 <yield/>
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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30 </requirements>
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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31 </xml>
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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32
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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33 <xml name="citations">
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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34 <citations>
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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35 <yield />
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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36 <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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37 <citation type="bibtex">
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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38 @misc{githubscanpy-scripts,
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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39 author = {Ni Huang, Krzysztof Polanski, EBI Gene Expression Team},
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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40 year = {2019},
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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41 title = {Monocle3-cli: command line interface for Monocle3},
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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42 publisher = {GitHub},
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43 journal = {GitHub repository},
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44 url = {https://github.com/ebi-gene-expression-group/monocle-scripts},
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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45 }</citation>
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46 </citations>
710d112ee525 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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47 </xml>
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48
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49 <xml name="input_object_params">
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50 <param name="input_object_file" argument="input-object-file" type="data" format="rdata" label="Input object in RDS format"/>
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51 <param name="input_object_format" argument="--input-object-format" type="select" label="Format of input object">
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52 <option value="cds3" selected="true">Monocle3 object in RDS</option>
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53 </param>
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54 </xml>
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55
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56 <xml name="output_object_params">
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57 <param name="output_object_format" argument="--output-object-format" type="select" label="Format of output object">
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58 <option value="cds3" selected="true">Monocle3 object in RDS</option>
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59 </param>
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60 <param name="introspective" argument="--introspective" type="boolean" checked="true" label="Print introspective information of output object"/>
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61 </xml>
1
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62
0
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63 <xml name="verbose_flag">
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64 <param name="verbose" argument="--verbose" type="boolean" checked="false" label="Emit verbose output"/>
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65 </xml>
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66 </macros>