Mercurial > repos > ebi-gxa > scanpy_find_cluster

annotate scanpy_macros.xml @ 0:2cb836f82ddb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
author ebi-gxa
date Wed, 13 Mar 2019 11:49:57 -0400
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children 5b33fec5d3cd
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0
2cb836f82ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
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1 <macros>
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2 <token name="@TOOL_VERSION@">1.3.2</token>
2cb836f82ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
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3 <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
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4 <token name="@PLOT_OPTS@">
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5 #if $do_plotting.plot
2cb836f82ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
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6 -P output.png
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7 --projectio $do_plotting.projection
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8 --components $do_plotting.components
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9 #if $do_plotting.color_by
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10 --color-by $do_plotting.color_by
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11 #end if
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12 #if $do_plotting.groups
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13 --group $do_plotting.groups
2cb836f82ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
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14 #end if
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15 #if $do_plotting.use_raw
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16 --use-raw
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17 #end if
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18 #if $do_plotting.palette
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19 --palette $do_plotting.palette
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20 #end if
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21 #if $do_plotting.edges
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22 --edges
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23 #end if
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24 #if $do_plotting.arrows
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25 --arrows
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26 #end if
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27 #if not $do_plotting.sort_order
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28 --no-sort-order
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29 #end if
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30 #if $do_plotting.frameoff
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31 --frameoff
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32 #end if
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33 #end if
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34 </token>
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35 <xml name="requirements">
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36 <requirements>
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37 <requirement type="package" version="0.0.5">scanpy-scripts</requirement>
2cb836f82ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
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38 <yield/>
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39 </requirements>
2cb836f82ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
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40 </xml>
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41 <token name="@VERSION_HISTORY@"><![CDATA[
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42 **Version history**
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43
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44 1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
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45 EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
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46 ]]></token>
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47 <xml name="citations">
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48 <citations>
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49 <citation type="doi">10.1186/s13059-017-1382-0</citation>
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50 <citation type="bibtex">
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51 @misc{githubscanpy-scripts,
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52 author = {Ni Huang, EBI Gene Expression Team},
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53 year = {2018},
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54 title = {Scanpy-scripts: command line interface for Scanpy},
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55 publisher = {GitHub},
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56 journal = {GitHub repository},
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57 url = {https://github.com/ebi-gene-expression-group/scanpy-scripts},
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58 }</citation>
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59 <yield />
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60 </citations>
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61 </xml>
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62 <xml name="input_object_params">
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63 <param name="input_obj_file" argument="--input-object-file" type="data" format="h5" label="Input object in hdf5 format"/>
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64 <param name="input_format" argument="--input-format" type="select" label="Format of input object">
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65 <option value="anndata" selected="true">AnnData format hdf5</option>
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66 <option value="loom">Loom format hdf5, current support is incomplete</option>
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67 </param>
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68 </xml>
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69 <xml name="output_object_params">
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70 <param name="output_format" argument="--output-format" type="select" label="Format of output object">
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71 <option value="anndata" selected="true">AnnData format hdf5</option>
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72 <option value="loom">Loom format hdf5, current support is defective</option>
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73 </param>
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74 </xml>
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75 <xml name="output_plot_params">
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76 <param name="color_by" argument="--color-by" type="text" value="n_genes" label="Color by attributes, comma separated strings"/>
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77 <param name="groups" argument="--groups" type="text" optional="ture" label="Restrict plotting to named groups, comma separated strings"/>
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78 <param name="projection" argument="--projection" type="select" label="Plot projection">
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79 <option value="2d" selected="true">2D</option>
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80 <option value="3d">3D</option>
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81 </param>
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82 <param name="components" argument="--components" type="text" value="1,2" label="Components to plot, comma separated integers"/>
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83 <param name="palette" argument="--palette" type="text" optional="true" label="Palette"/>
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84 <param name="use_raw" argument="--use-raw" type="boolean" checked="false" label="Use raw attributes if present"/>
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85 <param name="edges" argument="--edges" type="boolean" checked="false" label="Show edges"/>
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86 <param name="arrows" argument="--arrows" type="boolean" checked="false" label="Show arrows"/>
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87 <param name="sort_order" argument="--no-sort-order" type="boolean" checked="true" label="Element with high color-by value plot on top"/>
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88 <param name="frameoff" argument="--frameoff" type="boolean" checked="false" label="Omit frame"/>
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89 </xml>
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90 </macros>