Mercurial > repos > iuc > spapros

annotate macros.xml @ 0:c369fea6eab5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0
author iuc
date Sun, 25 Aug 2024 13:35:59 +0000
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c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0
iuc
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1 <macros>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0
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2 <token name="@TOOL_VERSION@">0.1.5</token>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0
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3 <token name="@VERSION_SUFFIX@">0</token>
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4 <token name="@profile@">22.05</token>
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5 <xml name="requirements">
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">spapros</requirement>
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8 <yield />
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9 </requirements>
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10 </xml>
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11 <xml name="creators">
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12 <creator>
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13 <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
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14 </creator>
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15 </xml>
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16 <xml name="citations">
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17 <citations>
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18 <citation type="doi">10.1101/2022.08.16.504115</citation>
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19 <citation type="doi">10.1093/gigascience/giaa102</citation>
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20 </citations>
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21 </xml>
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22 <xml name="version_command">
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23 <version_command><![CDATA[python -c "import spapros;print('%s' % spapros.__version__ )"]]></version_command>
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24 </xml>
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25 <token name="@CMD@"><![CDATA[
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26 cp '$adata' 'anndata.h5ad' &&
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27 cat '$script_file' > '$hidden_output' &&
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0
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28 python '$script_file' >> '$hidden_output' &&
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29 ls . >> '$hidden_output'
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0
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30 ]]>
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31 </token>
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32 <token name="@CMD_imports@"><![CDATA[
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33 import spapros as sp
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34 import os
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35 import pandas as pd
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36 import scanpy as sc
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37 import matplotlib as mpl
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38 import matplotlib.pyplot as plt
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39 import random
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40 ]]>
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41 </token>
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42 <token name="@CMD_plot@"><![CDATA[
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43 #if $method.set_ids != 'all' and $method.set_ids != '':
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44 set_ids=[$method.set_ids],
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45 #end if
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46 save='plot.$format',
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47 show=False
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48 ]]>
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49 </token>
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50 <xml name="set_ids">
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51 <param name="set_ids" type="text" value="all" optional="true" label="List of probeset ids (comma seperated, e.g., DE,HVG,random)" help="Kepp it with all or empty to select all probeset ids."/>
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52 </xml>
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53 <xml name="sanitize_query" token_validinitial="string.printable">
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54 <sanitizer>
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55 <valid initial="@VALIDINITIAL@">
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56 <remove value="&apos;" />
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57 </valid>
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58 </sanitizer>
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59 </xml>
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60 <xml name="sanitize_vectors" token_validinitial="string.digits">
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61 <sanitizer>
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62 <valid initial="@VALIDINITIAL@">
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63 <add value=","/>
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64 </valid>
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65 </sanitizer>
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66 </xml>
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67 <xml name="inputs_anndata">
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68 <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
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69 </xml>
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70 <token name="@CMD_read_inputs@"><![CDATA[
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71 adata = sc.read_h5ad('anndata.h5ad')
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72 ]]>
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73 </token>
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74 <xml name="inputs_common_advanced">
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75 <param name="show_log" type="boolean" checked="false" label="Output Log?" />
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76 </xml>
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77 <xml name="param_plot_format">
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78 <param name="format" type="select" label="Format for saving figures">
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79 <option value="png">png</option>
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80 <option value="pdf">pdf</option>
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81 <option value="svg">svg</option>
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82 </param>
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83 </xml>
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84 <xml name="param_markerset">
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85 <param name="markerset" type="data" format="tabular" label="Markerset tabular file with rows=conditions (e.g., celltypes) and column=features (e.g., genes)" help="This is beeing used to calculate the corelations betweens your probeset features and marker features. Marker features are for example genes that you know are important for your condition (e.g., celltypes)."/>
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86 <param name="header_markerset" type="select" optional="false" label="Header in the list of markers?">
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87 <option value="included">Header included</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0
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88 <option value="not_included">Header not included</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0
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89 </param>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0
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90 </xml>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0
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91 <xml name="hidden_outputs">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0
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92 <data name="hidden_output" format="txt" label="Log file" >
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0
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93 <filter>show_log</filter>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0
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94 </data>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0
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95 </xml>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0
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96 </macros>