Mercurial > repos > ebi-gxa > monocle3_diffexp
annotate monocle3-macros.xml @ 2:a7d4f80d1265 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8ef74a1abb7d22b5c18611b8cdd7a5bf56c51b10"
author | ebi-gxa |
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date | Tue, 03 Mar 2020 18:01:17 -0500 |
parents | f91ddb6bc4ff |
children | c5665e286bcf |
rev | line source |
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c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
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1 <macros> |
2
a7d4f80d1265
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8ef74a1abb7d22b5c18611b8cdd7a5bf56c51b10"
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2 <token name="@TOOL_VERSION@">0.1.4</token> |
a7d4f80d1265
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8ef74a1abb7d22b5c18611b8cdd7a5bf56c51b10"
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3 <token name="@PROFILE@">18.01</token> |
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c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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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> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
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5 <token name="@VERSION_HISTORY@"><![CDATA[ |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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6 **Version history** |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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7 |
2
a7d4f80d1265
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8ef74a1abb7d22b5c18611b8cdd7a5bf56c51b10"
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8 0.1.4+galaxy0: Updated to monocle3-cli 0.0.7 to fix bug with column headers in tsv. |
a7d4f80d1265
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8ef74a1abb7d22b5c18611b8cdd7a5bf56c51b10"
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9 |
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f91ddb6bc4ff
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. |
f91ddb6bc4ff
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 08ac0ad9182623944c4546f8ea8db6a1a537f7eb
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11 |
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c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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12 0.1.2+galaxy0: Initial version based on monocle3-cli 0.0.3 and monocle3 0.1.2 |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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13 ]]></token> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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14 <token name="@INPUT_OPTS@"> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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15 --input-object-format '${input_object_format}' '${input_object_file}' |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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16 </token> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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17 <token name="@OUTPUT_OPTS@"> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
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18 --output-object-format '${output_object_format}' output.RDS |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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19 #if $introspective |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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20 --introspective |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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21 #end if |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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22 </token> |
c0441ea8f37a
"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@"> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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24 #if $verbose |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
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25 --verbose |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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26 #end if |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
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27 </token> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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28 |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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29 <xml name="requirements"> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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30 <requirements> |
2
a7d4f80d1265
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8ef74a1abb7d22b5c18611b8cdd7a5bf56c51b10"
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31 <requirement type="package" version="0.0.7">monocle3-cli</requirement> |
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c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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32 <yield/> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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33 </requirements> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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34 </xml> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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35 |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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36 <xml name="citations"> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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37 <citations> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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38 <yield /> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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39 <citation type="doi">10.1038/nmeth.4402</citation> |
c0441ea8f37a
"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"> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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41 @misc{githubscanpy-scripts, |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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42 author = {Ni Huang, Krzysztof Polanski, EBI Gene Expression Team}, |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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43 year = {2019}, |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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44 title = {Monocle3-cli: command line interface for Monocle3}, |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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45 publisher = {GitHub}, |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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46 journal = {GitHub repository}, |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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47 url = {https://github.com/ebi-gene-expression-group/monocle-scripts}, |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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48 }</citation> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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49 </citations> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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50 </xml> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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51 |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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52 <xml name="input_object_params"> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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53 <param name="input_object_file" argument="input-object-file" type="data" format="rdata" label="Input object in RDS format"/> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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54 <param name="input_object_format" argument="--input-object-format" type="select" label="Format of input object"> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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55 <option value="cds3" selected="true">Monocle3 object in RDS</option> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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56 </param> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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57 </xml> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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58 |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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59 <xml name="output_object_params"> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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60 <param name="output_object_format" argument="--output-object-format" type="select" label="Format of output object"> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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61 <option value="cds3" selected="true">Monocle3 object in RDS</option> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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62 </param> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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63 <param name="introspective" argument="--introspective" type="boolean" checked="true" label="Print introspective information of output object"/> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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64 </xml> |
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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 08ac0ad9182623944c4546f8ea8db6a1a537f7eb
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65 |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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66 <xml name="verbose_flag"> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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67 <param name="verbose" argument="--verbose" type="boolean" checked="false" label="Emit verbose output"/> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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68 </xml> |
c0441ea8f37a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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69 </macros> |