Mercurial > repos > iuc > scanpy_plot

annotate plot.xml @ 17:2dfb2227a16c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
author iuc
date Sat, 14 Sep 2024 12:44:20 +0000
parents 1072ce66b426
children 40812a65a78b
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17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1 <tool id="scanpy_plot" name="Scanpy plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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2 <macros>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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3 <import>macros.xml</import>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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4 </macros>
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95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
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5 <expand macro="bio_tools"/>
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2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
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6 <expand macro="requirements">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
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7 <requirement type="package" version="3.9.1">matplotlib</requirement>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
8 <requirement type="package" version="0.13.2">seaborn</requirement>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
9 <requirement type="package" version="0.11.6">python-igraph</requirement>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
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10 </expand>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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11 <stdio>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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12 <regex match="... storing" source="stderr" level="warning"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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13 </stdio>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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14 <expand macro="version_command"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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15 <command detect_errors="exit_code"><![CDATA[
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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16 @CMD@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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17 ]]></command>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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18 <configfiles>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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19 <configfile name="script_file"><![CDATA[
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2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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20 @CMD_IMPORTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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21 @CMD_READ_INPUTS@
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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23 sc.settings.figdir = '.'
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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24
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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25 #if str($method.method) == 'pl.scatter':
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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26
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
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27 #if str($method.type.type) == 'xy':
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95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
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28 x_field='$method.type.x'
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
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29 y_field='$method.type.y'
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
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30
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 16
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31 #if $method.type.log:
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95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
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parents: 10
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32 if x_field in adata.obs or x_field in adata.var:
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
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33 if x_field in adata.obs:
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
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parents: 10
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34 adata.obs[f"log_{x_field}"] = np.log10(adata.obs[x_field])
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
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35 elif x_field in adata.var:
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
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36 adata.var[f"log_{x_field}"] = np.log10(adata.var[x_field])
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
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37 x_field=f"log_{x_field}"
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
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parents: 10
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38
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
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39 if y_field in adata.obs or y_field in adata.var:
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
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40 if y_field in adata.obs:
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
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41 adata.obs[f"log_{y_field}"] = np.log10(adata.obs[y_field])
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
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42 elif y_field in adata.var:
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
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43 adata.var[f"log_{y_field}"] = np.log10(adata.var[y_field])
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
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44 y_field=f"log_{y_field}"
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2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
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45 #end if
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 16
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46 #end if
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
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47
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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48 sc.pl.scatter(
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2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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49 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
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50 #if str($method.type.type) == 'xy':
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
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51 x=x_field,
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
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52 y=y_field,
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2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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53 #if str($method.type.color) != '':
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7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
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54 color='$method.type.color',
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2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
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55 #end if
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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56 #if str('$method.type.layers.use_layers') == 'true':
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e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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57 layers=('$method.type.layers.layer_x', '$method.type.layers.layer_y', '$method.type.layers.layer_color'),
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2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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58 #end if
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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59 #else if str($method.type.type) == 'basis':
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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60 basis='$method.type.basis',
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2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
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61 #if str($method.type.color) != '':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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62 #set $color = ([x.strip() for x in str($method.type.color).split(',')])
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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63 color=$color,
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2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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64 #end if
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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65 #end if
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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66 use_raw=$method.use_raw,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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67 sort_order=$method.sort_order,
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2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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68 @CMD_PARAM_GROUPS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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69 @CMD_PARAM_PL_COMPONENTS@
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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70 projection='$method.plot.projection',
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2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 16
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71 #if str($method.plot.legend_loc) != '':
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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72 legend_loc='$method.plot.legend_loc',
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2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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73 #end if
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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74 @CMD_PARAM_LEGEND_FONTSIZE@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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75 legend_fontweight='$method.plot.legend_fontweight',
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 16
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76 #if $method.plot.color_map:
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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77 color_map='$method.plot.color_map',
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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78 #end if
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 16
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79 #if $method.plot.palette:
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6adf98e782f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec"
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80 palette=['$method.plot.palette'],
7
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
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81 #end if
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82 frameon=$method.plot.frameon,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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83 @CMD_PARAM_SIZE@
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84 @CMD_PARAM_TITLE@
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85 @CMD_SHOW_NONE@)
0
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86
17
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diff changeset
87 #else if str($method.method) == 'pl.heatmap':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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88 @CMD_VAR_NAMES_HEADER_CHECK@
0
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89 sc.pl.heatmap(
17
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90 @CMD_PARAM_PLOT_INPUTS@
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parents: 16
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91 @CMD_PARAMS_INPUTS@
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iuc
parents: 16
diff changeset
92 @CMD_PARAM_GENE_SYMBOLS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
93 @CMD_PARAMS_PLOTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
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94 @CMD_PARAMS_PL_HEATMAP@
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iuc
parents: 16
diff changeset
95 @CMD_SHOW_NONE@)
0
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96
17
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diff changeset
97 #else if str($method.method) == 'pl.dotplot':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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98 @CMD_VAR_NAMES_HEADER_CHECK@
0
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99 sc.pl.dotplot(
17
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100 @CMD_PARAM_PLOT_INPUTS@
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101 @CMD_PARAMS_INPUTS@
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102 @CMD_PARAM_GENE_SYMBOLS@
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103 @CMD_PARAMS_PLOTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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104 @CMD_PL_DOTPLOT@
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105 @CMD_SHOW_NONE@)
0
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106
17
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107 #else if str($method.method) == 'pl.tracksplot':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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108 @CMD_VAR_NAMES_HEADER_CHECK@
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109 sc.pl.tracksplot(
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110 @CMD_PARAM_PLOT_INPUTS@
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111 @CMD_PARAMS_INPUTS@
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iuc
parents: 16
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112 @CMD_PARAM_GENE_SYMBOLS@
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113 @CMD_PARAMS_PLOTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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114 @CMD_SHOW_NONE@)
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115
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116 #else if str($method.method) == 'pl.violin':
0
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117 sc.pl.violin(
17
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118 @CMD_PARAM_PLOT_INPUTS@
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119 #if str($method.key_variables.type) == 'var_names':
0
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120 #set $key_list = adata.var_names
17
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121 #else if str($method.key_variables.type) == 'obs':
0
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122 #set $key_list = adata.obs.select_dtypes(exclude=['category']).columns
17
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123 #else if str($method.key_variables.type) == 'custom':
0
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124 #set $key_list=([x.strip() for x in str($method.key_variables.keys).split(',')])
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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125 #end if
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126 keys=$key_list,
17
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127 #if str($method.groupby) != '':
0
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128 groupby='$method.groupby',
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129 #end if
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130 log=$method.log,
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131 use_raw=$method.use_raw,
17
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132 @CMD_CONDITIONAL_STRIPPLOT@
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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133 multi_panel=$method.violin_plot.multi_panel.multi_panel,
17
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134 ##if $method.violin_plot.multi_panel.multi_panel == "True" and str($method.violin_plot.multi_panel.width) != '' and str($method.violin_plot.multi_panel.height) != ''
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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135 ##figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height),
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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136 ##end if
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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137 #if str($method.xlabel) != '':
0
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138 xlabel='$method.xlabel',
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139 #end if
17
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140 #if str($method.rotation) != '':
0
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141 rotation=$method.rotation,
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142 #end if
17
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143 @CMD_PARAMS_SEABORN_VIOLINPLOT@
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144 @CMD_PARAM_LAYER@
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145 @CMD_SHOW_NONE@)
0
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146
17
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147 #else if str($method.method) == 'pl.stacked_violin':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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148 @CMD_VAR_NAMES_HEADER_CHECK@
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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149 sc.pl.stacked_violin(
17
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150 @CMD_PARAM_PLOT_INPUTS@
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151 @CMD_PARAMS_INPUTS@
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parents: 16
diff changeset
152 @CMD_PARAM_GENE_SYMBOLS@
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153 @CMD_PARAMS_PLOTS@
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154 @CMD_PARAMS_PL_STACKED_VIOLIN@
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155 @CMD_SHOW_NONE@)
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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156
17
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157 #else if str($method.method) == 'pl.matrixplot':
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158 @CMD_VAR_NAMES_HEADER_CHECK@
0
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159 sc.pl.matrixplot(
17
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160 @CMD_PARAM_PLOT_INPUTS@
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diff changeset
161 @CMD_PARAMS_INPUTS@
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diff changeset
162 @CMD_PARAM_GENE_SYMBOLS@
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diff changeset
163 @CMD_PARAMS_PLOTS@
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iuc
parents: 16
diff changeset
164 @CMD_PARAMS_PL_MATRIXPLOT@
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165 @CMD_SHOW_NONE@)
0
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166
17
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167 #else if str($method.method) == 'pl.clustermap':
0
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168 sc.pl.clustermap(
17
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169 #if str($method.use_raw) == 'True':
0
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170 adata=adata.X,
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171 #else
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172 adata=adata,
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173 #end if
17
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174 #if str($method.obs_keys) != '':
0
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175 obs_keys='$method.obs_keys',
1
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176 #end if
0
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177 use_raw=$method.use_raw,
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178 method='$method.seaborn_clustermap.method',
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179 metric='$method.seaborn_clustermap.metric',
17
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180 #if str($method.seaborn_clustermap.z_score) != 'None':
0
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181 z_score=$method.seaborn_clustermap.z_score,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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182 #end if
17
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diff changeset
183 #if str($method.seaborn_clustermap.standard_scale) != 'None':
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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184 standard_scale=$method.seaborn_clustermap.standard_scale,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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parents:
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185 #end if
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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186 col_cluster=$method.seaborn_clustermap.col_cluster,
17
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187 row_cluster=$method.seaborn_clustermap.row_cluster,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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188 save='.$format',
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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189 @CMD_SHOW_NONE@)
0
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190
17
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diff changeset
191 #else if str($method.method) == 'pl.highest_expr_genes':
0
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iuc
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192 sc.pl.highest_expr_genes(
17
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193 @CMD_PARAM_PLOT_INPUTS@
0
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194 n_top=$method.n_top,
17
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195 @CMD_PARAM_GENE_SYMBOLS@
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iuc
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196 #if str($method.setseaborn_boxplot.color) != '':
0
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197 color='$method.setseaborn_boxplot.color',
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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198 #end if
17
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iuc
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diff changeset
199 #if $method.setseaborn_boxplot.palette:
0
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iuc
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200 palette='$method.setseaborn_boxplot.palette',
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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201 #end if
17
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iuc
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diff changeset
202 saturation=$method.setseaborn_boxplot.saturation,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
203 @CMD_SHOW_NONE@)
0
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204
17
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diff changeset
205 #else if str($method.method) == 'pl.highly_variable_genes':
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
206 sc.pl.highly_variable_genes(
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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207 adata_or_result=adata,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
208 log=$method.log,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
209 save='.$format',
17
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iuc
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diff changeset
210 highly_variable_genes=$method.highly_variable_genes,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
211 @CMD_SHOW_NONE@)
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
212
17
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diff changeset
213 #else if str($method.method) == 'pl.scrublet_score_distribution':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
214 sc.pl.scrublet_score_distribution(
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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diff changeset
215 adata=adata,
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iuc
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diff changeset
216 scale_hist_obs='$method.scale_hist_obs',
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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diff changeset
217 scale_hist_sim='$method.scale_hist_sim',
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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diff changeset
218 @CMD_PARAMS_FIGSIZE@
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parents: 16
diff changeset
219 save='.$format',
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
220 @CMD_SHOW_NONE@)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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diff changeset
221
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
222 #else if str($method.method) == 'pl.pca':
0
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iuc
parents:
diff changeset
223 sc.pl.pca(
17
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iuc
parents: 16
diff changeset
224 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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diff changeset
225 @CMD_PARAM_COLOR@
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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226 use_raw=$method.use_raw,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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227 sort_order=$method.sort_order,
17
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228 @CMD_PARAM_GROUPS@
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iuc
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diff changeset
229 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@
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iuc
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diff changeset
230 @CMD_SCATTER_OUTINE@
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iuc
parents: 16
diff changeset
231 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@
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diff changeset
232 @CMD_PARAM_LAYER@
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233 @CMD_SHOW_NONE@)
0
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234
17
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diff changeset
235 #else if str($method.method) == 'pl.pca_loadings':
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diff changeset
236 sc.pl.pca_loadings(
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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diff changeset
237 @CMD_PARAM_PLOT_INPUTS@
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238 #set $components = ([int(x.strip()) for x in str($method.components).split(',')])
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diff changeset
239 components=$components,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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diff changeset
240 include_lowest=$method.include_lowest,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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diff changeset
241 #if str($method.n_points) != '':
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iuc
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diff changeset
242 n_points=$method.n_points,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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diff changeset
243 #end if
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iuc
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diff changeset
244 @CMD_SHOW_NONE@)
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diff changeset
245
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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diff changeset
246 #else if str($method.method) == 'pl.pca_variance_ratio':
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
247 sc.pl.pca_variance_ratio(
17
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248 @CMD_PARAM_PLOT_INPUTS@
0
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iuc
parents:
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249 n_pcs=$method.n_pcs,
17
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diff changeset
250 log=$method.log,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
251 @CMD_SHOW_NONE@)
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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252
17
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diff changeset
253 #else if str($method.method) == 'pl.pca_overview':
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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diff changeset
254 sc.pl.pca_overview(
17
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diff changeset
255 @CMD_PARAM_PLOT_INPUTS@
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iuc
parents: 16
diff changeset
256 @CMD_PARAM_COLOR@
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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257 use_raw=$method.use_raw,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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258 sort_order=$method.sort_order,
17
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iuc
parents: 16
diff changeset
259 @CMD_PARAM_GROUPS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
260 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
261 @CMD_SCATTER_OUTINE@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
262 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@
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iuc
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diff changeset
263 @CMD_SHOW_NONE@)
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
264
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
265 #else if str($method.method) == 'pl.tsne':
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
266 sc.pl.tsne(
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
267 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
268 @CMD_PARAM_COLOR@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
269 @CMD_PARAM_GENE_SYMBOLS@
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
270 use_raw=$method.use_raw,
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
271 @CMD_PL_EDGES@
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
272 arrows=$method.arrows,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
273 sort_order=$method.sort_order,
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
274 @CMD_PARAM_GROUPS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
275 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
276 @CMD_SCATTER_OUTINE@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
277 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
278 @CMD_PARAM_LAYER@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
279 @CMD_SHOW_NONE@)
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
280
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
281 #else if str($method.method) == 'pl.umap':
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
282 sc.pl.umap(
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
283 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
284 @CMD_PARAM_COLOR@
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
285 use_raw=$method.use_raw,
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
286 @CMD_PL_EDGES@
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
287 arrows=$method.arrows,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
288 sort_order=$method.sort_order,
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
289 @CMD_PARAM_GROUPS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
290 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
291 @CMD_SCATTER_OUTINE@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
292 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
293 @CMD_PARAM_LAYER@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
294 @CMD_SHOW_NONE@)
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
295
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
296 #else if str($method.method) == 'pl.diffmap':
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
297 sc.pl.diffmap(
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
298 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
299 @CMD_PARAM_COLOR@
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
300 use_raw=$method.use_raw,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
301 sort_order=$method.sort_order,
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
302 @CMD_PARAM_GROUPS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
303 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
304 @CMD_SCATTER_OUTINE@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
305 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
306 @CMD_PARAM_LAYER@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
307 @CMD_SHOW_NONE@)
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
308
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
309 #else if str($method.method) == 'pl.draw_graph':
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
310 sc.pl.draw_graph(
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
311 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
312 @CMD_PARAM_COLOR@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
313 @CMD_PARAM_GENE_SYMBOLS@
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
314 use_raw=$method.use_raw,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
315 layout='$method.layout',
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
316 @CMD_PL_EDGES@
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
317 arrows=$method.arrows,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
318 sort_order=$method.sort_order,
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
319 @CMD_PARAM_GROUPS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
320 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
321 @CMD_SCATTER_OUTINE@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
322 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
323 @CMD_PARAM_LAYER@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
324 @CMD_SHOW_NONE@)
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
325
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
326 #else if str($method.method) == 'pl.embedding_density':
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
327 sc.pl.embedding_density(
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
328 @CMD_PARAM_PLOT_INPUTS@
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
329 basis='$method.basis',
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
330 #if str($method.key) != '':
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
331 key='$method.key',
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
332 #end if
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
333 #if str($method.groupby) != '':
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
334 groupby='$method.groupby',
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
335 #end if
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
336 #if str($method.group) != '':
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
337 #set $group = ([x.strip() for x in str($method.group).split(',')])
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
338 group=$group,
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
339 #end if
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
340 #if $method.color_map:
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
341 color_map='$method.color_map',
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
342 #end if
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
343 bg_dotsize=$method.bg_dotsize,
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
344 fg_dotsize=$method.fg_dotsize,
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
345 ncols=$method.ncols,
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
346 wspace=$method.wspace,
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
347 hspace=$method.hspace,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
348 @CMD_SHOW_NONE@)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
349
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
350
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
351
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
352 #else if str($method.method) == 'pl.dpt_timeseries':
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
353 sc.pl.dpt_timeseries(
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
354 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
355 #if str($method.heatmap.as_heatmap) == 'True'
12
9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0
iuc
parents: 11
diff changeset
356 #if $method.heatmap.color_map
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
357 color_map='$method.heatmap.color_map',
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
358 #end if
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
359 #end if
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
360 as_heatmap=$method.heatmap.as_heatmap,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
361 @CMD_SHOW_NONE@)
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
362
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
363 #else if str($method.method) == 'pl.paga':
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
364 sc.pl.paga(
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
365 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
366 @CMD_PARAMS_PL_PAGA@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
367 @CMD_SHOW_NONE@)
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
368
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
369 #else if str($method.method) == 'pl.paga_compare':
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
370 sc.pl.paga_compare(
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
371 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
372 @CMD_PARAMS_PL_PAGA@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
373 @CMD_PARAM_PL_COMPONENTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
374 projection='$method.plot.projection',
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
375 #if str($method.plot.legend_loc) != '':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
376 legend_loc='$method.plot.legend_loc',
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
377 #end if
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
378 @CMD_PARAM_LEGEND_FONTSIZE@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
379 legend_fontweight='$method.plot.legend_fontweight',
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
380 #if $method.plot.color_map:
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
381 color_map='$method.plot.color_map',
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
382 #end if
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
383 #if $method.plot.palette:
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
384 palette=['$method.plot.palette'],
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
385 #end if
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
386 @CMD_PARAM_SIZE@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
387 @CMD_PARAM_TITLE@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
388 @CMD_SHOW_NONE@)
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
389
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
390 #else if str($method.method) == 'pl.paga_path':
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
391 sc.pl.paga_path(
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
392 @CMD_PARAM_PLOT_INPUTS@
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
393 #set $nodes = ([int(x.strip()) for x in str($method.nodes).split(',')])
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
394 nodes=$nodes,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
395 #set $keys=([x.strip() for x in str($method.keys).split(',')])
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
396 keys=$keys,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
397 use_raw=$method.use_raw,
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
398 #if str($method.annotations) != '':
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
399 #set $annotations=([x.strip() for x in str($method.annotations).split(',')])
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
400 annotations=$annotations,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
401 #end if
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
402 #if $method.color_map:
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
403 color_map='$method.color_map',
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
404 #end if
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
405 n_avg=$method.n_avg,
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
406 #if str($method.annotations) != '':
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
407 groups_key='$method.groups_key',
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
408 #end if
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
409 as_heatmap=$method.as_heatmap,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
410 show_node_names=$method.show_node_names,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
411 show_colorbar=$method.show_colorbar,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
412 show_yticks=$method.show_yticks,
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
413 normalize_to_zero_one=$method.normalize_to_zero_one,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
414 @CMD_SHOW_NONE@)
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
415
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
416 #else if str($method.method) == 'pl.rank_genes_groups':
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
417 sc.pl.rank_genes_groups(
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
418 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
419 @CMD_PARAM_GROUPS@
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
420 n_genes=$method.n_genes,
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
421 @CMD_PARAM_GENE_SYMBOLS@
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
422 fontsize=$method.fontsize,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
423 ncols=$method.ncols,
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
424 sharey=$method.sharey,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
425 @CMD_SHOW_NONE@)
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
426
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
427 #else if $method.method == 'pl.rank_genes_groups_violin'
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
428 sc.pl.rank_genes_groups_violin(
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
429 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
430 @CMD_PARAM_GROUPS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
431 #if str($method.genes.select) == 'n_genes':
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
432 n_genes=$method.genes.n_genes,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
433 #else
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
434 #set $gene_names = ([x.strip() for x in str($method.genes.gene_names).split(',')])
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
435 gene_names=$gene_names,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
436 #end if
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
437 @CMD_PARAM_GENE_SYMBOLS@
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
438 use_raw=$method.use_raw,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
439 split=$method.split,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
440 strip=$method.violin_plot.stripplot.stripplot,
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
441 #if str($method.violin_plot.stripplot.stripplot) == 'True':
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
442 jitter=$method.violin_plot.stripplot.jitter.jitter,
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
443 #if str($method.violin_plot.stripplot.jitter.jitter) == 'True':
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
444 size=$method.violin_plot.stripplot.jitter.size,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
445 #end if
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
446 #end if
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
447 density_norm='$method.violin_plot.density_norm',
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
448 @CMD_SHOW_NONE@)
16
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
449
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
450 #else if str($method.method) == 'pl.rank_genes_groups_stacked_violin':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
451 @CMD_VAR_NAMES_HEADER_CHECK@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
452 sc.pl.rank_genes_groups_stacked_violin(
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
453 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
454 @CMD_PL_RANK_GENES_GROUPS_EXT@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
455 @CMD_PARAMS_PLOTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
456 @CMD_PARAM_GENE_SYMBOLS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
457 @CMD_PARAMS_PL_STACKED_VIOLIN@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
458 @CMD_SHOW_NONE@)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
459
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
460 #else if str($method.method) == 'pl.rank_genes_groups_heatmap':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
461 @CMD_VAR_NAMES_HEADER_CHECK@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
462 sc.pl.rank_genes_groups_heatmap(
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
463 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
464 @CMD_PL_RANK_GENES_GROUPS_EXT@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
465 @CMD_PARAMS_PLOTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
466 @CMD_PARAM_GENE_SYMBOLS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
467 @CMD_PARAMS_PL_HEATMAP@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
468 @CMD_SHOW_NONE@)
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
469
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
470 #else if str($method.method) == 'pl.rank_genes_groups_dotplot':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
471 @CMD_VAR_NAMES_HEADER_CHECK@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
472 sc.pl.rank_genes_groups_dotplot(
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
473 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
474 @CMD_PL_RANK_GENES_GROUPS_EXT@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
475 @CMD_PARAMS_PLOTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
476 @CMD_PARAM_GENE_SYMBOLS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
477 @CMD_PL_DOTPLOT@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
478 @CMD_VALUES_TO_PLOT@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
479 @CMD_SHOW_NONE@)
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
480
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
481 #else if str($method.method) == 'pl.rank_genes_groups_matrixplot':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
482 @CMD_VAR_NAMES_HEADER_CHECK@
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
483 sc.pl.rank_genes_groups_matrixplot(
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
484 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
485 @CMD_PL_RANK_GENES_GROUPS_EXT@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
486 @CMD_PARAMS_PLOTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
487 @CMD_PARAM_GENE_SYMBOLS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
488 @CMD_PARAMS_PL_MATRIXPLOT@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
489 @CMD_VALUES_TO_PLOT@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
490 @CMD_SHOW_NONE@)
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
491
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
492 #else if str($method.method) == 'pl.rank_genes_groups_tracksplot':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
493 @CMD_VAR_NAMES_HEADER_CHECK@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
494 sc.pl.rank_genes_groups_tracksplot(
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
495 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
496 @CMD_PL_RANK_GENES_GROUPS_EXT@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
497 @CMD_PARAMS_PLOTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
498 @CMD_PARAM_GENE_SYMBOLS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
499 @CMD_PARAMS_PL_HEATMAP@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
500 @CMD_SHOW_NONE@)
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
501
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
502 #end if
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
503 ]]></configfile>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
504 </configfiles>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
505 <inputs>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
506 <expand macro="inputs_anndata"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
507 <expand macro="param_plot_format"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
508 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
509 <param argument="method" type="select" label="Method used for plotting">
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
510 <option value="pl.scatter">Generic: Scatter plot along observations or variables axes, using 'pl.scatter'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
511 <option value="pl.heatmap">Generic: Heatmap of the expression values of set of genes, using 'pl.heatmap'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
512 <option value="pl.dotplot">Generic: Makes a dot plot of the expression values, using 'pl.dotplot'</option>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
513 <option value="pl.tracksplot">Generic: Makes a tracks plot of the expression values per cell, using 'pl.tracksplot'</option>
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
514 <option value="pl.violin">Generic: Violin plot, using 'pl.violin'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
515 <option value="pl.stacked_violin">Generic: Stacked violin plots, using 'pl.stacked_violin'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
516 <option value="pl.matrixplot">Generic: Heatmap of the mean expression values per cluster, using 'pl.matrixplot'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
517 <option value="pl.clustermap">Generic: Hierarchically-clustered heatmap, using 'pl.clustermap'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
518 <option value="pl.highest_expr_genes">Preprocessing: Plot the fraction of counts assigned to each gene over all cells, using 'pl.highest_expr_genes'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
519 <option value="pl.highly_variable_genes">Preprocessing: Plot dispersions versus means for genes, using 'pl.highly_variable_genes'</option>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
520 <option value="pl.scrublet_score_distribution">Preprocessing: Plot histogram of doublet scores, using 'pl.scrublet_score_distribution'</option>
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
521 <option value="pl.pca">PCA: Scatter plot in PCA coordinates, using 'pl.pca'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
522 <option value="pl.pca_loadings">PCA: Rank genes according to contributions to PCs, using 'pl.pca_loadings'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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parents: 2
diff changeset
523 <option value="pl.pca_variance_ratio">PCA: Scatter plot in PCA coordinates, using 'pl.pca_variance_ratio'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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parents: 2
diff changeset
524 <option value="pl.pca_overview">PCA: Plot PCA results, using 'pl.pca_overview'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
525 <option value="pl.tsne">Embeddings: Scatter plot in tSNE basis, using 'pl.tsne'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
526 <option value="pl.umap">Embeddings: Scatter plot in UMAP basis, using 'pl.umap'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
527 <option value="pl.diffmap">Embeddings: Scatter plot in Diffusion Map basis, using 'pl.diffmap'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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parents: 2
diff changeset
528 <option value="pl.draw_graph">Embeddings: Scatter plot in graph-drawing basis, using 'pl.draw_graph'</option>
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parents: 10
diff changeset
529 <option value="pl.embedding_density">Embeddings: Plot the density of cells in an embedding (per condition), using 'pl.embedding_density'</option>
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parents: 16
diff changeset
530 <!-- This function is commented out because it is not compatible with pandas version. If the issue is not resolved in the next update, this should be removed. -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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diff changeset
531 <!-- <option value="pl.dpt_groups_pseudotime">Branching trajectories and pseudotime, clustering: Plot groups and pseudotime, using 'pl.dpt_groups_pseudotime'</option> -->
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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parents: 2
diff changeset
532 <option value="pl.dpt_timeseries">Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series, using 'pl.dpt_timeseries'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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parents: 2
diff changeset
533 <option value="pl.paga">Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges, using 'pl.paga'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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parents: 2
diff changeset
534 <option value="pl.paga_compare">Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side, using 'pl.paga_compare'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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parents: 2
diff changeset
535 <option value="pl.paga_path">Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths, using 'pl.paga_path'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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parents: 2
diff changeset
536 <option value="pl.rank_genes_groups">Marker genes: Plot ranking of genes using dotplot plot, using 'pl.rank_genes_groups'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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parents: 2
diff changeset
537 <option value="pl.rank_genes_groups_violin">Marker genes: Plot ranking of genes as violin plot, using 'pl.rank_genes_groups_violin'</option>
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parents: 16
diff changeset
538 <option value="pl.rank_genes_groups_stacked_violin">Marker genes: Plot ranking of genes as stacked violin plot, using 'pl.rank_genes_groups_stacked_violin'</option>
3
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parents: 2
diff changeset
539 <option value="pl.rank_genes_groups_heatmap">Marker genes: Plot ranking of genes as heatmap plot, using 'pl.rank_genes_groups_heatmap'</option>
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parents: 16
diff changeset
540 <option value="pl.rank_genes_groups_dotplot">Marker genes: Plot ranking of genes as dotplot plot, using 'pl.rank_genes_groups_dotplot'</option>
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
541 <option value="pl.rank_genes_groups_matrixplot">Marker genes: Plot ranking of genes as matrixplot plot, using 'pl.rank_genes_groups_matrixplot'</option>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
542 <option value="pl.rank_genes_groups_tracksplot">Marker genes: Plot ranking of genes as tracksplot plot, using 'pl.rank_genes_groups_tracksplot'</option>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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543 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
544 <when value="pl.scatter">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
545 <conditional name="type">
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diff changeset
546 <param name="type" type="select" label="Plotting tool that computed coordinates">
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diff changeset
547 <option value="xy" selected="true">Using coordinates</option>
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diff changeset
548 <option value="basis">Using tool that computes coordinates</option>
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diff changeset
549 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
550 <when value="xy">
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parents: 6
diff changeset
551 <param argument="x" type="text" value="" label="x coordinate" help="Index or key from either '.obs' or '.var'">
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parents: 16
diff changeset
552 <expand macro="sanitize_query"/>
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parents: 6
diff changeset
553 </param>
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diff changeset
554 <param argument="y" type="text" value="" label="y coordinate" help="Index or key from either '.obs' or '.var'">
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parents: 16
diff changeset
555 <expand macro="sanitize_query"/>
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parents: 6
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556 </param>
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parents: 10
diff changeset
557 <expand macro="param_log"/>
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parents: 6
diff changeset
558 <param argument="color" type="text" value="" label="Color by" help="Color points by single variable in `.obs` or `.var`">
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parents: 16
diff changeset
559 <expand macro="sanitize_query"/>
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parents: 6
diff changeset
560 </param>
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parents: 0
diff changeset
561 <conditional name="layers">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
562 <param argument="use_layers" type="select" label="Use the layers attribute?">
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diff changeset
563 <option value="false" selected="true">No</option>
1
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parents: 0
diff changeset
564 <option value="true">Yes</option>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
565 </param>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
566 <when value="true">
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parents: 6
diff changeset
567 <param argument="layer_x" type="text" value="" optional="true" label="Layers for x coordinate" help="Use the 'layers' attribute of 'adata' if present">
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parents: 16
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568 <expand macro="sanitize_query"/>
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parents: 6
diff changeset
569 </param>
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
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diff changeset
570 <param argument="layer_y" type="text" value="" optional="true" label="Layers for y coordinate" help="Use the 'layers' attribute of 'adata' if present">
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parents: 16
diff changeset
571 <expand macro="sanitize_query"/>
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parents: 6
diff changeset
572 </param>
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parents: 6
diff changeset
573 <param argument="layer_color" type="text" value="" optional="true" label="Layers for color" help="Use the 'layers' attribute of 'adata' if present">
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parents: 16
diff changeset
574 <expand macro="sanitize_query"/>
7
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parents: 6
diff changeset
575 </param>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
576 </when>
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parents: 0
diff changeset
577 <when value="false"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
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578 </conditional>
0
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579 </when>
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580 <when value="basis">
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parents: 16
diff changeset
581 <param argument="basis" type="select" label="Plotting tool that computes coordinates">
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582 <option value="pca">pca (need to run on 'pl.pca' output)</option>
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parents: 2
diff changeset
583 <option value="tsne">tsne (need to run on 'tl.tsne' output)</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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parents: 2
diff changeset
584 <option value="umap">umap (need to run on 'tl.umap' output)</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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parents: 2
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585 <option value="diffmap">diffmap (need to run on 'tl.diffmap' output)</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
586 <option value="draw_graph_fr">draw_graph_fr (need to run on 'tl.draw_graph' output)</option>
0
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parents:
diff changeset
587 </param>
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parents:
diff changeset
588 <expand macro="param_color"/>
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589 </when>
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590 </conditional>
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parents: 16
diff changeset
591 <expand macro="param_use_raw" falsevalue="None"/>
0
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592 <param argument="sort_order" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot data points with higher values on top of others?" help="For continuous annotations used as color parameter"/>
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parents: 2
diff changeset
593 <expand macro="param_groups"/>
0
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594 <section name="plot" title="Plot attributes">
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parents: 16
diff changeset
595 <expand macro="param_pl_components"/>
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parents:
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596 <expand macro="param_projection"/>
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parents:
diff changeset
597 <expand macro="param_legend_loc"/>
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parents:
diff changeset
598 <expand macro="param_legend_fontsize"/>
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parents:
diff changeset
599 <expand macro="param_legend_fontweight"/>
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600 <expand macro="param_color_map"/>
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parents:
diff changeset
601 <expand macro="param_palette"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
602 <expand macro="param_frameon"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
603 <expand macro="param_size"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
604 <expand macro="param_title"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
605 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
606 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
607 <when value="pl.heatmap">
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
608 <expand macro="params_inputs"/>
17
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iuc
parents: 16
diff changeset
609 <expand macro="param_gene_symbols"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
610 <expand macro="params_plots"/>
17
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iuc
parents: 16
diff changeset
611 <expand macro="params_pl_heatmap"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
612 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
613 <when value="pl.dotplot">
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
614 <expand macro="params_inputs"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
615 <expand macro="param_gene_symbols"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
616 <expand macro="params_plots"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
617 <expand macro="params_pl_dotplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
618 </when>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
619 <when value="pl.tracksplot">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
620 <expand macro="params_inputs"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
621 <expand macro="param_gene_symbols"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
622 <expand macro="params_plots"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
623 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
624 <when value="pl.violin">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
625 <conditional name="key_variables">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
626 <param name="type" type="select" label="Keys for accessing variables">
17
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parents: 16
diff changeset
627 <option value="var_names" selected="true">All variables in '.var_names'</option>
3
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iuc
parents: 2
diff changeset
628 <option value="obs">All fields in '.obs'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
629 <option value="custom">Subset of variables in 'adata.var_names' or fields of '.obs'</option>
0
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iuc
parents:
diff changeset
630 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
631 <when value="var_names"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
632 <when value="obs"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
633 <when value="custom">
7
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parents: 6
diff changeset
634 <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from '.var_names' or fields of '.obs'">
17
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iuc
parents: 16
diff changeset
635 <expand macro="sanitize_query"/>
7
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
parents: 6
diff changeset
636 </param>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
637 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
638 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
639 <expand macro="param_groupby"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
640 <expand macro="param_log"/>
17
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iuc
parents: 16
diff changeset
641 <expand macro="param_use_raw" falsevalue="None"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
642 <section name="violin_plot" title="Violin plot attributes">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
643 <expand macro="conditional_stripplot"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
644 <conditional name="multi_panel">
3
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iuc
parents: 2
diff changeset
645 <param argument="multi_panel" type="select" label="Display keys in multiple panels" help="Also when 'groupby is not provided">
17
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parents: 16
diff changeset
646 <option value="None" selected="true">No</option>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
647 <option value="True">Yes</option>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
648 </param>
17
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iuc
parents: 16
diff changeset
649 <when value="None"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
650 <when value="True">
17
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iuc
parents: 16
diff changeset
651 <!-- <param argument="width" type="integer" min="0" value="" optional="true" label="Width of the figure"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
652 <param argument="height" type="integer" min="0" value="" optional="true" label="Height of the figure"/> -->
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
653 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
654 </conditional>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
655 </section>
7
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iuc
parents: 6
diff changeset
656 <param argument="xlabel" type="text" value="" optional="true" label="Label of the x axis" help="Defaults to 'groupby' if 'rotation' is 'None', otherwise, no label is shown.">
17
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iuc
parents: 16
diff changeset
657 <expand macro="sanitize_query"/>
7
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
parents: 6
diff changeset
658 </param>
17
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iuc
parents: 16
diff changeset
659 <param argument="rotation" type="float" value="" optional="true" label="Rotation of xtick labels"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
660 <expand macro="params_seaborn_violinplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
661 <expand macro="param_layer"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
662 </when>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
663 <when value="pl.stacked_violin">
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
664 <expand macro="params_inputs"/>
17
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iuc
parents: 16
diff changeset
665 <expand macro="param_gene_symbols"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
666 <expand macro="params_plots"/>
17
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iuc
parents: 16
diff changeset
667 <expand macro="params_pl_stacked_violin"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
668 </when>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
669 <when value="pl.matrixplot">
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
670 <expand macro="params_inputs"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
671 <expand macro="param_gene_symbols"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
672 <expand macro="params_plots"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
673 <expand macro="params_pl_matrixplot"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
674 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
675 <when value="pl.clustermap">
7
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
parents: 6
diff changeset
676 <param argument="obs_keys" type="text" value="" optional="true" label="Categorical annotation to plot with a different color map" help="Currently, only a single key is supported.">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
677 <expand macro="sanitize_query"/>
7
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
parents: 6
diff changeset
678 </param>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
679 <expand macro="param_use_raw"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
680 <section name="seaborn_clustermap" title="Parameters for seaborn.clustermap">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
681 <param name="method" type="select" label="Linkage method to use for calculating clusters" help="More details in https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
682 <option value="average" selected="true">average: UPGMA algorithm</option>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
683 <option value="single">single: Nearest Point Algorithm</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
684 <option value="complete">complete: Farthest Point Algorithm or Voor Hees Algorithm</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
685 <option value="weighted">weighted: WPGMA algorithm</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
686 <option value="centroid">centroid: UPGMC algorithm</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
687 <option value="median">median: WPGMC algorithm</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
688 <option value="ward">ward: incremental algorithm</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
689 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
690 <param name="metric" type="select" label="Distance metric to use for the data" help="See scipy.spatial.distance.pdist documentation for more options https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.pdist.html">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
691 <expand macro="distance_metric_options"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
692 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
693 <param name="z_score" type="select" label="Calculate z-scores for the rows or the columns?" help="Z scores are: z = (x - mean)/std, so values in each row (column) will get the mean of the row (column) subtracted, then divided by the standard deviation of the row (column). This ensures that each row (column) has mean of 0 and variance of 1.">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
694 <option value="None" selected="true">No Z-score</option>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
695 <option value="0">Rows</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
696 <option value="1">Columns</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
697 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
698 <param name="standard_scale" type="select" label="Standardize a dimension?" help="It means for each row or column, subtract the minimum and divide each by its maximum.">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
699 <option value="None" selected="true">No standardization</option>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
700 <option value="0">Rows</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
701 <option value="1">Columns</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
702 </param>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
703 <param name="col_cluster" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Cluster the columns?"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
704 <param name="row_cluster" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Cluster the rows?"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
705 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
706 </when>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
707 <when value="pl.highest_expr_genes">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
708 <param argument="n_top" type="integer" min="0" value="30" label="Number of top genes"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
709 <expand macro="param_gene_symbols"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
710 <expand macro="param_log"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
711 <section name="setseaborn_boxplot" title="Plot settings" expanded="false">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
712 <param argument="color" type="text" value="" optional="true" label="Color for all of the elements, or seed for a gradient palette">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
713 <expand macro="sanitize_query"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
714 </param>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
715 <param argument="palette" type="select" optional="true" label="Colors to use for the different levels of the hue variable" help="See https://seaborn.pydata.org/tutorial/color_palettes.html for more details.">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
716 <expand macro="seaborn_color_palette_options"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
717 </param>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
718 <param argument="saturation" type="float" value="0.75" label="Proportion of the original saturation to draw colors at" help="Large patches often look better with slightly desaturated colors, but set this to 1 if you want the plot colors to perfectly match the input color spec."/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
719 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
720 </when>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
721 <when value="pl.highly_variable_genes">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
722 <expand macro="param_log"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
723 <param argument="highly_variable_genes" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot highly variable genes or gene subset?"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
724 </when>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
725 <when value="pl.scrublet_score_distribution">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
726 <param name="scale_hist_obs" type="select" label="Set y axis scale transformation in matplotlib for the plot of observed transcriptomes">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
727 <option value="log" selected="true">log</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
728 <option value="linear">linear</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
729 <option value="symlog">symlog</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
730 <option value="logit">logit</option>
7
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
parents: 6
diff changeset
731 </param>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
732 <param name="scale_hist_sim" type="select" label="Set y axis scale transformation in matplotlib for the plot of simulated doublets">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
733 <option value="linear" selected="true">linear</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
734 <option value="log">log</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
735 <option value="symlog">symlog</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
736 <option value="logit">logit</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
737 </param>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
738 <expand macro="pl_figsize"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
739 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
740 <when value="pl.pca">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
741 <expand macro="param_color"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
742 <expand macro="param_use_raw"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
743 <expand macro="param_sort_order"/>
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
744 <expand macro="param_groups"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
745 <expand macro="params_pl_attribute_section"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
746 <expand macro="params_scatter_outine"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
747 <expand macro="section_matplotlib_pyplot_scatter"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
748 <expand macro="param_layer"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
749 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
750 <when value="pl.pca_loadings">
7
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
parents: 6
diff changeset
751 <param argument="components" type="text" value="1,2,3" label="List of comma-separated components" help="1, 2, 3 means first, second and third principal components">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
752 <expand macro="sanitize_query"/>
7
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
parents: 6
diff changeset
753 </param>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
754 <param argument="include_lowest" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Show the variables with both highest and lowest loadings"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
755 <param argument="n_points" type="integer" value="" optional="true" label="Number of variables to plot for each component"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
756 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
757 <when value="pl.pca_variance_ratio">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
758 <param argument="n_pcs" type="integer" min="0" value="30" label="Number of PCs to show"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
759 <expand macro="param_log"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
760 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
761 <when value="pl.pca_overview">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
762 <expand macro="param_color"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
763 <expand macro="param_use_raw"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
764 <expand macro="param_sort_order"/>
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
765 <expand macro="param_groups"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
766 <expand macro="params_pl_attribute_section"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
767 <expand macro="params_scatter_outine"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
768 <expand macro="section_matplotlib_pyplot_scatter"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
769 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
770 <when value="pl.tsne">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
771 <expand macro="param_color"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
772 <expand macro="param_gene_symbols"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
773 <expand macro="param_use_raw"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
774 <expand macro="pl_edges"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
775 <expand macro="param_arrows"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
776 <expand macro="param_sort_order"/>
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
777 <expand macro="param_groups"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
778 <expand macro="params_pl_attribute_section"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
779 <expand macro="params_scatter_outine"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
780 <expand macro="section_matplotlib_pyplot_scatter"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
781 <expand macro="param_layer"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
782 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
783 <when value="pl.umap">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
784 <expand macro="param_color"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
785 <expand macro="param_use_raw"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
786 <expand macro="pl_edges"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
787 <expand macro="param_arrows"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
788 <expand macro="param_sort_order"/>
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
789 <expand macro="param_groups"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
790 <expand macro="params_pl_attribute_section"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
791 <expand macro="params_scatter_outine"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
792 <expand macro="section_matplotlib_pyplot_scatter"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
793 <expand macro="param_layer"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
794 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
795 <when value="pl.diffmap">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
796 <expand macro="param_color"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
797 <expand macro="param_use_raw"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
798 <expand macro="param_sort_order"/>
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
799 <expand macro="param_groups"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
800 <expand macro="params_pl_attribute_section"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
801 <expand macro="params_scatter_outine"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
802 <expand macro="section_matplotlib_pyplot_scatter"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
803 <expand macro="param_layer"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
804 </when>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
805 <when value="pl.draw_graph">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
806 <expand macro="param_color"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
807 <expand macro="param_gene_symbols"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
808 <expand macro="param_use_raw"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
809 <param argument="layout" type="select" optional="false" label="Plotting layout">
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
810 <expand macro="options_layout"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
811 </param>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
812 <expand macro="pl_edges"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
813 <expand macro="param_arrows"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
814 <expand macro="param_sort_order"/>
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
815 <expand macro="param_groups"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
816 <expand macro="params_pl_attribute_section"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
817 <expand macro="params_scatter_outine"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
818 <expand macro="section_matplotlib_pyplot_scatter"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
819 <expand macro="param_layer"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
820 </when>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
821 <when value="pl.embedding_density">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
822 <param argument="basis" type="text" value="umap" label="The embedding over which the density was calculated." help="This embedded representation should be found in adata.obsm['X_[basis]']">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
823 <expand macro="sanitize_query"/>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
824 </param>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
825 <param argument="key" type="text" optional="true" value="" label="Name of the .obs covariate that contains the density estimates" help="Alternatively, pass _groupby_.">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
826 <expand macro="sanitize_query"/>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
827 </param>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
828 <param argument="groupby" type="text" optional="true" value="" label="Name of the condition used in tl.embedding_density" help="Alternatively, pass _key_.">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
829 <expand macro="sanitize_query"/>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
830 </param>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
831 <param argument="group" type="text" optional="all" value="" label="The category in the categorical observation annotation to be plotted"
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
832 help="For example, 'G1' in the cell cycle 'phase' covariate. If multiple categories want to be plotted use a comma separated list">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
833 <expand macro="sanitize_query"/>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
834 </param>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
835 <expand macro="param_color_map"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
836 <param argument="bg_dotsize" type="integer" min="0" value="80" label="Dot size for background data points not in the group"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
837 <param argument="fg_dotsize" type="integer" min="0" value="180" label="Dot size for foreground data points in the group"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
838 <expand macro="param_ncols"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
839 <expand macro="param_wspace"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
840 <expand macro="param_hspace"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
841 </when>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
842 <!-- This function is commented out because it is not compatible with pandas version. If the issue is not resolved in the next update, this should be removed. -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
843 <!-- <when value="pl.dpt_groups_pseudotime">
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
844 <expand macro="param_color_map"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
845 </when> -->
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
846 <when value="pl.dpt_timeseries">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
847 <conditional name="heatmap">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
848 <param argument="as_heatmap" type="select" label="Plot the timeseries as heatmap?">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
849 <option value="True" selected="true">Yes</option>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
850 <option value="False">No</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
851 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
852 <when value="True">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
853 <expand macro="param_color_map"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
854 </when>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
855 <when value="False"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
856 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
857 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
858 <when value="pl.paga">
17
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iuc
parents: 16
diff changeset
859 <expand macro="params_pl_paga"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
860 </when>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
861 <when value="pl.paga_compare">
17
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iuc
parents: 16
diff changeset
862 <expand macro="params_pl_paga"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
863 <section name="plot" title="Plot attributes">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
864 <expand macro="param_pl_components"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
865 <expand macro="param_projection"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
866 <expand macro="param_legend_loc">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 16
diff changeset
867 <option value="on data">on data</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 16
diff changeset
868 <option value="right margin">right margin</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 16
diff changeset
869 </expand>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
870 <expand macro="param_legend_fontsize"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
871 <expand macro="param_legend_fontweight"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
872 <expand macro="param_color_map"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
873 <expand macro="param_palette"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 16
diff changeset
874 <expand macro="param_frameon"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 16
diff changeset
875 <expand macro="param_size"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 16
diff changeset
876 <expand macro="param_title"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 16
diff changeset
877 </section>
1
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iuc
parents: 0
diff changeset
878 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
879 <when value="pl.paga_path">
17
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parents: 16
diff changeset
880 <param argument="nodes" type="text" value="" label="A path through nodes of the abstracted graph" help="Each node is represented by its indice (within .categories) for the groups that have been used to run PAGA. Comma-separated">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 16
diff changeset
881 <expand macro="sanitize_query"/>
7
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iuc
parents: 6
diff changeset
882 </param>
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parents: 6
diff changeset
883 <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from '.var_names' or fields of '.obs'">
17
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parents: 16
diff changeset
884 <expand macro="sanitize_query"/>
7
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parents: 6
diff changeset
885 </param>
1
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parents: 0
diff changeset
886 <expand macro="param_use_raw"/>
17
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parents: 16
diff changeset
887 <param argument="annotations" type="text" value="dpt_pseudotime" optional="true" label="Key to plot" help="Keys for obs, comma-separated">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 16
diff changeset
888 <expand macro="sanitize_query"/>
7
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parents: 6
diff changeset
889 </param>
1
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parents: 0
diff changeset
890 <expand macro="param_color_map"/>
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parents: 0
diff changeset
891 <param argument="n_avg" type="integer" value="1" label="Number of data points to include in computation of running average"/>
7
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parents: 6
diff changeset
892 <param argument="groups_key" type="text" value="" optional="true" label="Key of the grouping used to run PAGA" help="If not set, use uns/page/groups">
17
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parents: 16
diff changeset
893 <expand macro="sanitize_query"/>
7
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parents: 6
diff changeset
894 </param>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
895 <param argument="as_heatmap" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot the timeseries as heatmap?" help="If not, annotations have no effect."/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
896 <param argument="show_node_names" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot the node names on the nodes bar?"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
897 <param argument="show_colorbar" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Show the colorbar?"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
898 <param argument="show_yticks" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Show the y ticks?"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
899 <param argument="normalize_to_zero_one" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Shift and scale the running average to [0, 1] per gene?"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
900 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
901 <when value="pl.rank_genes_groups">
3
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iuc
parents: 2
diff changeset
902 <expand macro="param_groups"/>
17
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iuc
parents: 16
diff changeset
903 <expand macro="param_n_genes" value="20"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 16
diff changeset
904 <expand macro="param_gene_symbols"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
905 <param argument="fontsize" type="integer" min="0" value="8" label="Font size for gene names"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
906 <expand macro="param_ncols"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
907 <param argument="sharey" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Should the y-axis of each panels be shared?" help="If not, each panel has its own y-axis range"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
908 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
909 <when value="pl.rank_genes_groups_violin">
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
910 <expand macro="param_groups"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
911 <conditional name="genes">
17
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iuc
parents: 16
diff changeset
912 <param argument="select" type="select" label="Which genes to plot?">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
913 <option value="n_genes" selected="true">A number of genes</option>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
914 <option value="gene_names">A custom list of genes</option>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
915 </param>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
916 <when value="n_genes">
17
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parents: 16
diff changeset
917 <expand macro="param_n_genes" value="20"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
918 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
919 <when value="gene_names">
7
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iuc
parents: 6
diff changeset
920 <param argument="gene_names" type="text" value="" label="List of genes to plot" help="A list of comma-separated names">
17
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iuc
parents: 16
diff changeset
921 <expand macro="sanitize_query"/>
7
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
parents: 6
diff changeset
922 </param>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
923 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
924 </conditional>
17
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iuc
parents: 16
diff changeset
925 <expand macro="param_gene_symbols"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
926 <expand macro="param_use_raw" falsevalue="None"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
927 <param argument="split" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Split the violins?"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
928 <section name="violin_plot" title="Violin plot attributes">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
929 <expand macro="conditional_stripplot"/>
17
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iuc
parents: 16
diff changeset
930 <param argument="density_norm" type="select" label="Method used to scale the width of each violin">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
931 <option value="width" selected="true">width: each violin will have the same width</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
932 <option value="area">area: each violin will have the same area</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
933 <option value="count">count: the width of the violins will be scaled by the number of observations in that bin</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
934 </param>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
935 </section>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
936 </when>
17
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iuc
parents: 16
diff changeset
937 <when value="pl.rank_genes_groups_stacked_violin">
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
938 <expand macro="pl_rank_genes_groups_ext"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
939 <expand macro="params_plots"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
940 <expand macro="param_gene_symbols"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
941 <expand macro="params_pl_stacked_violin"/>
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
942 </when>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
943 <when value="pl.rank_genes_groups_heatmap">
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
944 <expand macro="pl_rank_genes_groups_ext"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
945 <expand macro="params_plots"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
946 <expand macro="param_gene_symbols"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
947 <expand macro="params_pl_heatmap"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
948 </when>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
949 <when value="pl.rank_genes_groups_dotplot">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
950 <expand macro="pl_rank_genes_groups_ext"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
951 <expand macro="params_plots"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
952 <expand macro="param_gene_symbols"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
953 <expand macro="params_pl_dotplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
954 <expand macro="values_to_plot"/>
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
955 </when>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
956 <when value="pl.rank_genes_groups_matrixplot">
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
957 <expand macro="pl_rank_genes_groups_ext"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
958 <expand macro="params_plots"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
959 <expand macro="param_gene_symbols"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
960 <expand macro="params_pl_matrixplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
961 <expand macro="values_to_plot"/>
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
962 </when>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
963 <when value="pl.rank_genes_groups_tracksplot">
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
964 <expand macro="pl_rank_genes_groups_ext"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
965 <expand macro="params_plots"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
966 <expand macro="param_gene_symbols"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
967 <expand macro="params_pl_heatmap"/>
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
968 </when>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
969 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
970 <expand macro="inputs_common_advanced"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
971 </inputs>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
972 <outputs>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
973 <data name="out_png" format="png" from_work_dir="*.png" label="PNG plot from ${tool.name} (${method.method}) on ${on_string}">
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
974 <filter>format == 'png' and method['method'] != 'pl.rank_genes_groups_violin'</filter>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
975 </data>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
976 <collection name="collection_png" type="list" label="PNG plots from ${tool.name} (${method.method}) on ${on_string}">
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
977 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).png" format="png"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
978 <filter>format == 'png' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
979 </collection>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
980 <data name="out_pdf" format="pdf" from_work_dir="*.pdf" label="PDF plot from ${tool.name} (${method.method}) on ${on_string}">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
981 <filter>format == 'pdf' and method['method'] != 'pl.rank_genes_groups_violin'</filter>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
982 </data>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
983 <collection name="collection_pdf" type="list" label="PDF plots from ${tool.name} (${method.method}) on ${on_string}">
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
984 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).pdf" format="pdf"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
985 <filter>format == 'pdf' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
986 </collection>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
987 <data name="out_svg" format="svg" from_work_dir="*.svg" label="SVG plot from ${tool.name} (${method.method}) on ${on_string}">
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
988 <filter>format == 'svg' and method['method'] != pl.rank_genes_groups_violin</filter>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
989 </data>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
990 <collection name="collection_svg" type="list" label="SVG plots from ${tool.name} (${method.method}) on ${on_string}">
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
991 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).svg" format="svg"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
992 <filter>format == 'svg' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
993 </collection>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
994 <data name="hidden_output" format="txt" label="Log file" hidden="true" >
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
995 <filter>advanced_common['show_log']</filter>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
996 </data>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
997 </outputs>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
998 <tests>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
999 <!-- test 1 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1000 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1001 <param name="adata" value="pbmc68k_reduced.h5ad"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1002 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1003 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1004 <param name="method" value="pl.scatter"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1005 <conditional name="type">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1006 <param name="type" value="basis"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1007 <param name="basis" value="umap"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1008 <param name="color" value="HES4"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1009 </conditional>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1010 <param name="use_raw" value="True"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1011 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1012 <param name="legend_fontsize" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1013 <param name="legend_fontweight" value="normal"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1014 <param name="color_map" value="inferno"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1015 <param name="palette" value="inferno"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1016 <param name="size" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1017 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1018 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1019 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1020 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1021 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1022 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1023 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1024 <has_text_matching expression="sc.pl.scatter"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1025 <has_text_matching expression="basis='umap'"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1026 <has_text_matching expression="color=\['HES4'\]"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1027 <has_text_matching expression="use_raw=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1028 <has_text_matching expression="sort_order=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1029 <has_text_matching expression="projection='2d'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1030 <has_text_matching expression="legend_fontsize=1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1031 <has_text_matching expression="legend_fontweight='normal'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1032 <has_text_matching expression="color_map='inferno'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1033 <has_text_matching expression="frameon=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1034 <has_text_matching expression="size=1.0"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1035 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1036 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1037 <output name="out_png" file="pl.scatter.umap.pbmc68k_reduced.png" ftype="png" compare="image_diff"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1038 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1039
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1040 <!-- test 2 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1041 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1042 <param name="adata" value="krumsiek11.h5ad"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1043 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1044 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1045 <param name="method" value="pl.scatter"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1046 <conditional name="type">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1047 <param name="type" value="xy"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1048 <param name="x" value="EKLF"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1049 <param name="y" value="Cebpa"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1050 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1051 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1052 <param name="legend_fontsize" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1053 <param name="legend_fontweight" value="normal"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1054 <param name="palette" value="bwr"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1055 <param name="size" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1056 <param name="title" value="A title"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1057 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1058 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1059 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1060 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1061 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1062 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1063 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1064 <has_text_matching expression="sc.pl.scatter"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1065 <has_text_matching expression="x_field='EKLF'"/>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1066 <has_text_matching expression="y_field='Cebpa'"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1067 <has_text_matching expression="use_raw=None"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1068 <has_text_matching expression="sort_order=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1069 <has_text_matching expression="projection='2d'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1070 <has_text_matching expression="legend_fontsize=1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1071 <has_text_matching expression="legend_fontweight='normal'"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1072 <has_text_matching expression="frameon=True"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1073 <has_text_matching expression="size=1.0"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1074 <has_text_matching expression="title='A title'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1075 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1076 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1077 <output name="out_png" file="pl.scatter.krumsiek11.png" ftype="png" compare="image_diff"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1078 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1079
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1080 <!-- test 3 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1081 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1082 <param name="adata" value="pbmc68k_reduced.h5ad"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1083 <param name="format" value="png"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1084 <conditional name="method">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1085 <param name="method" value="pl.scatter"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1086 <conditional name="type">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1087 <param name="type" value="xy"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1088 <param name="x" value="n_genes"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1089 <param name="y" value="n_counts"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1090 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1091 <section name="plot">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1092 <param name="legend_fontsize" value="1"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1093 <param name="legend_fontweight" value="normal"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1094 <param name="palette" value="bwr"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1095 <param name="size" value="1"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1096 <param name="title" value="A title"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1097 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1098 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1099 <section name="advanced_common">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1100 <param name="show_log" value="true"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1101 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1102 <output name="hidden_output">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1103 <assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1104 <has_text_matching expression="sc.pl.scatter"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1105 <has_text_matching expression="use_raw=None"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1106 <has_text_matching expression="sort_order=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1107 <has_text_matching expression="projection='2d'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1108 <has_text_matching expression="legend_fontsize=1"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1109 <has_text_matching expression="legend_fontweight='normal'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1110 <has_text_matching expression="frameon=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1111 <has_text_matching expression="size=1.0"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1112 <has_text_matching expression="title='A title'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1113 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1114 </output>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1115 <output name="out_png" file="pl.scatter.pbmc68k_reduced.png" ftype="png" compare="image_diff"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1116 </test>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1117
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1118 <!-- test 4 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1119 <test expect_num_outputs="2">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1120 <param name="adata" value="krumsiek11.h5ad"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1121 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1122 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1123 <param name="method" value="pl.heatmap"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1124 <param name="groupby" value="cell_type"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1125 <conditional name="figsize">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1126 <param name="custom" value="yes"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1127 <param name="width" value="10"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1128 <param name="height" value="3"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1129 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1130 <param name="dendrogram" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1131 <param name="swap_axes" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1132 <section name="matplotlib_pyplot_imshow">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1133 <param name="cmap" value="YlGnBu"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1134 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1135 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1136 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1137 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1138 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1139 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1140 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1141 <has_text_matching expression="sc.pl.heatmap"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1142 <has_text_matching expression="var_names=adata.var_names"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1143 <has_text_matching expression="groupby='cell_type'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1144 <has_text_matching expression="log=False"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1145 <has_text_matching expression="use_raw=None"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1146 <has_text_matching expression="num_categories=7"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1147 <has_text_matching expression="dendrogram=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1148 <has_text_matching expression="figsize=\(10, 3\)"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1149 <has_text_matching expression="swap_axes=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1150 <has_text_matching expression="show_gene_labels=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1151 <has_text_matching expression="cmap='YlGnBu'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1152 <has_text_matching expression="origin='upper'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1153 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1154 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1155 <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="image_diff"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1156 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1157
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1158 <!-- test 5 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1159 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1160 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1161 <param name="format" value="png"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1162 <conditional name="method">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1163 <param name="method" value="pl.heatmap"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1164 <conditional name="var_names">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1165 <param name="type" value="custom"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1166 <param name="var_names" value="Fog1,EKLF,SCL"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1167 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1168 <param name="gene_symbols" value="symbol"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1169 <param name="groupby" value="cell_type"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1170 <conditional name="figsize">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1171 <param name="custom" value="yes"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1172 <param name="width" value="10"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1173 <param name="height" value="3"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1174 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1175 <param name="dendrogram" value="True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1176 <param name="swap_axes" value="True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1177 <param name="show_gene_labels" value="True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1178 <section name="matplotlib_pyplot_imshow">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1179 <param name="cmap" value="YlGnBu"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1180 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1181 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1182 <section name="advanced_common">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1183 <param name="show_log" value="true"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1184 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1185 <output name="hidden_output">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1186 <assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1187 <has_text_matching expression="sc.pl.heatmap"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1188 <has_text_matching expression="gene_symbols='symbol'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1189 <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1190 <has_text_matching expression="groupby='cell_type'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1191 <has_text_matching expression="log=False"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1192 <has_text_matching expression="use_raw=None"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1193 <has_text_matching expression="num_categories=7"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1194 <has_text_matching expression="dendrogram=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1195 <has_text_matching expression="figsize=\(10, 3\)"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1196 <has_text_matching expression="swap_axes=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1197 <has_text_matching expression="show_gene_labels=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1198 <has_text_matching expression="cmap='YlGnBu'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1199 <has_text_matching expression="origin='upper'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1200 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1201 </output>
9
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927"
iuc
parents: 8
diff changeset
1202 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1203
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1204 <!-- test 6 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1205 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1206 <param name="adata" value="pbmc68k_reduced.h5ad"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1207 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1208 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1209 <param name="method" value="pl.dotplot"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1210 <conditional name="var_names">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1211 <param name="type" value="custom"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1212 <param name="var_names" value="CD79A, MS4A1, CD8A, CD8B, LYZ, GNLY, NKG7, RP3-467N11.1, FCGR3A, FCER1A, CST3, POU2AF1, LINC00402"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1213 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1214 <param name="groupby" value="louvain"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1215 <param name="dendrogram" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1216 <repeat name="var_group_positions">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1217 <param name="start" value="0"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1218 <param name="end" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1219 <param name="label" value="B cells"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1220 </repeat>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1221 <repeat name="var_group_positions">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1222 <param name="start" value="11"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1223 <param name="end" value="12"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1224 <param name="label" value="dendritic"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1225 </repeat>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1226 <param name="color_map" value="hot"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1227 <param name="dot_max" value="0.7"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1228 <param name="dot_min" value="0.1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1229 <section name="matplotlib_pyplot_scatter">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1230 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1231 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1232 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1233 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1234 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1235 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1236 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1237 <has_text_matching expression="sc.pl.dotplot"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1238 <has_text_matching expression="var_names=\['CD79A', 'MS4A1', 'CD8A', 'CD8B', 'LYZ', 'GNLY', 'NKG7', 'RP3-467N11.1', 'FCGR3A', 'FCER1A', 'CST3', 'POU2AF1', 'LINC00402'\]"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1239 <has_text_matching expression="groupby='louvain'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1240 <has_text_matching expression="log=False"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1241 <has_text_matching expression="use_raw=None"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1242 <has_text_matching expression="num_categories=7"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1243 <has_text_matching expression="dendrogram=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1244 <has_text_matching expression="var_group_positions=\[\(0, 1\), \(11, 12\)\]"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1245 <has_text_matching expression="var_group_labels=\['B cells', 'dendritic'\]"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1246 <has_text_matching expression="color_map='hot'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1247 <has_text_matching expression="dot_max=0.7"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1248 <has_text_matching expression="dot_min=0.1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1249 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1250 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1251 <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="image_diff"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1252 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1253
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1254 <!-- test 7 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1255 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1256 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1257 <param name="format" value="png"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1258 <conditional name="method">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1259 <param name="method" value="pl.dotplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1260 <conditional name="var_names">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1261 <param name="type" value="custom"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1262 <param name="var_names" value="Fog1,EKLF,SCL"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1263 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1264 <param name="gene_symbols" value="symbol"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1265 <param name="groupby" value="cell_type"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1266 <param name="dendrogram" value="True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1267 <section name="matplotlib_pyplot_imshow">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1268 <param name="cmap" value="YlGnBu"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1269 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1270 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1271 <section name="advanced_common">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1272 <param name="show_log" value="true"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1273 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1274 <output name="hidden_output">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1275 <assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1276 <has_text_matching expression="sc.pl.dotplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1277 <has_text_matching expression="gene_symbols='symbol'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1278 <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1279 <has_text_matching expression="groupby='cell_type'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1280 <has_text_matching expression="log=False"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1281 <has_text_matching expression="use_raw=None"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1282 <has_text_matching expression="num_categories=7"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1283 <has_text_matching expression="dendrogram=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1284 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1285 </output>
9
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927"
iuc
parents: 8
diff changeset
1286 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1287
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1288 <!-- test 8 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1289 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1290 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1291 <param name="format" value="png"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1292 <conditional name="method">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1293 <param name="method" value="pl.tracksplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1294 <param name="gene_symbols" value="symbol"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1295 <param name="groupby" value="cell_type"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1296 <param name="dendrogram" value="True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1297 <section name="matplotlib_pyplot_imshow">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1298 <param name="cmap" value="YlGnBu"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1299 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1300 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1301 <section name="advanced_common">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1302 <param name="show_log" value="true"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1303 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1304 <output name="hidden_output">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1305 <assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1306 <has_text_matching expression="sc.pl.tracksplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1307 <has_text_matching expression="gene_symbols='symbol'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1308 <has_text_matching expression="groupby='cell_type'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1309 <has_text_matching expression="log=False"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1310 <has_text_matching expression="use_raw=None"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1311 <has_text_matching expression="num_categories=7"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1312 <has_text_matching expression="dendrogram=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1313 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1314 </output>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1315 </test>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1316
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1317 <!-- test 9 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1318 <test expect_num_outputs="2">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1319 <param name="adata" value="pbmc68k_reduced.h5ad"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1320 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1321 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1322 <param name="method" value="pl.violin"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1323 <conditional name="key_variables">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1324 <param name="type" value="custom"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1325 <param name="keys" value="n_genes, percent_mito, n_counts"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1326 </conditional>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1327 <section name="violin_plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1328 <conditional name="multi_panel">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1329 <param name="multi_panel" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1330 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1331 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1332 <section name="seaborn_violinplot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1333 <param name="linewidth" value="0"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1334 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1335 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1336 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1337 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1338 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1339 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1340 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1341 <has_text_matching expression="sc.pl.violin"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1342 <has_text_matching expression="keys=\['n_genes', 'percent_mito', 'n_counts'\]"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1343 <has_text_matching expression="log=False"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1344 <has_text_matching expression="use_raw=None"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1345 <has_text_matching expression="stripplot=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1346 <has_text_matching expression="jitter=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1347 <has_text_matching expression="size=1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1348 <has_text_matching expression="multi_panel=True"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1349 <has_text_matching expression="bw_method='scott'"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1350 <has_text_matching expression="saturation=0.75"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1351 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1352 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1353 <output name="out_png" file="pl.violin.pbmc68k_reduced_custom.png" ftype="png" compare="image_diff" eps="0.4"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1354 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1355
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1356 <!-- test 10 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1357 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1358 <param name="adata" value="krumsiek11.h5ad"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1359 <param name="format" value="png"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1360 <conditional name="method">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1361 <param name="method" value="pl.stacked_violin"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1362 <param name="groupby" value="cell_type"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1363 <param name="dendrogram" value="True"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1364 <param name="swap_axes" value="True"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1365 <section name="violin_plot">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1366 <param name="density_norm" value="width"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1367 </section>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1368 <section name="seaborn_violinplot">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1369 <param name="linewidth" value="0"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1370 </section>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1371 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1372 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1373 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1374 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1375 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1376 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1377 <has_text_matching expression="sc.pl.stacked_violin"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1378 <has_text_matching expression="groupby='cell_type'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1379 <has_text_matching expression="log=False"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1380 <has_text_matching expression="use_raw=None"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1381 <has_text_matching expression="num_categories=7"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1382 <has_text_matching expression="dendrogram=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1383 <has_text_matching expression="swap_axes=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1384 <has_text_matching expression="stripplot=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1385 <has_text_matching expression="jitter=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1386 <has_text_matching expression="size=1"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1387 <has_text_matching expression="density_norm='width'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1388 <has_text_matching expression="bw_method='scott'"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1389 <has_text_matching expression="saturation=0.75"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1390 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1391 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1392 <output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="image_diff" eps="1.1"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1393 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1394
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1395 <!-- test 11 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1396 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1397 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1398 <param name="format" value="png"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1399 <conditional name="method">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1400 <param name="method" value="pl.stacked_violin"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1401 <conditional name="var_names">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1402 <param name="type" value="custom"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1403 <param name="var_names" value="Fog1,EKLF,SCL"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1404 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1405 <param name="gene_symbols" value="symbol"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1406 <param name="groupby" value="cell_type"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1407 <param name="dendrogram" value="True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1408 <param name="swap_axes" value="True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1409 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1410 <section name="advanced_common">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1411 <param name="show_log" value="true"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1412 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1413 <output name="hidden_output">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1414 <assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1415 <has_text_matching expression="sc.pl.stacked_violin"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1416 <has_text_matching expression="gene_symbols='symbol'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1417 <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1418 <has_text_matching expression="groupby='cell_type'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1419 <has_text_matching expression="log=False"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1420 <has_text_matching expression="use_raw=None"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1421 <has_text_matching expression="num_categories=7"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1422 <has_text_matching expression="dendrogram=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1423 <has_text_matching expression="swap_axes=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1424 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1425 </output>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1426 <output name="out_png" file="pl.stacked_violin_pp.filter_genes_dispersion.krumsiek11-seurat.png" compare="image_diff" eps="0.6"/>
9
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927"
iuc
parents: 8
diff changeset
1427 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1428
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1429 <!-- test 12 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1430 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1431 <param name="adata" value="krumsiek11.h5ad"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1432 <param name="format" value="png"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1433 <conditional name="method">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1434 <param name="method" value="pl.matrixplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1435 <param name="groupby" value="cell_type"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1436 <param name="dendrogram" value="True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1437 <param name="swap_axes" value="True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1438 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1439 <section name="advanced_common">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1440 <param name="show_log" value="true"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1441 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1442 <output name="hidden_output">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1443 <assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1444 <has_text_matching expression="sc.pl.matrixplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1445 <has_text_matching expression="var_names=adata.var_names"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1446 <has_text_matching expression="groupby='cell_type'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1447 <has_text_matching expression="log=False"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1448 <has_text_matching expression="use_raw=None"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1449 <has_text_matching expression="num_categories=7"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1450 <has_text_matching expression="dendrogram=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1451 <has_text_matching expression="swap_axes=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1452 <has_text_matching expression="snap=False"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1453 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1454 </output>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1455 <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="image_diff"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1456 </test>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1457
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1458 <!-- test 13 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1459 <test expect_num_outputs="2">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1460 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1461 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1462 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1463 <param name="method" value="pl.matrixplot"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1464 <conditional name="var_names">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1465 <param name="type" value="custom"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1466 <param name="var_names" value="Fog1,EKLF,SCL"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1467 </conditional>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1468 <param name="gene_symbols" value="symbol"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1469 <param name="groupby" value="cell_type"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1470 <conditional name="figsize">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1471 <param name="custom" value="yes"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1472 <param name="width" value="10"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1473 <param name="height" value="3"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1474 </conditional>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1475 <param name="dendrogram" value="True"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1476 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1477 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1478 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1479 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1480 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1481 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1482 <has_text_matching expression="sc.pl.matrixplot"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1483 <has_text_matching expression="gene_symbols='symbol'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1484 <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1485 <has_text_matching expression="groupby='cell_type'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1486 <has_text_matching expression="log=False"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1487 <has_text_matching expression="use_raw=None"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1488 <has_text_matching expression="num_categories=7"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1489 <has_text_matching expression="dendrogram=True"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1490 <has_text_matching expression="swap_axes=False"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1491 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1492 </output>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1493 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1494
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1495 <!-- test 14 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1496 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1497 <param name="adata" value="krumsiek11.h5ad"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1498 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1499 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1500 <param name="method" value="pl.clustermap"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1501 <section name="seaborn_clustermap">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1502 <param name="method" value="single"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1503 <param name="col_cluster" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1504 <param name="row_cluster" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1505 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1506 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1507 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1508 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1509 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1510 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1511 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1512 <has_text_matching expression="sc.pl.clustermap"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1513 <has_text_matching expression="adata=adata"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1514 <has_text_matching expression="use_raw=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1515 <has_text_matching expression="method='single'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1516 <has_text_matching expression="metric='euclidean'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1517 <has_text_matching expression="col_cluster=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1518 <has_text_matching expression="row_cluster=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1519 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1520 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1521 <output name="out_png" file="pl.clustermap.krumsiek11.png" ftype="png" compare="image_diff"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1522 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1523
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1524 <!-- test 15 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1525 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1526 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1527 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1528 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1529 <param name="method" value="pl.highest_expr_genes"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1530 <param name="gene_symbols" value="symbol"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1531 <section name="setseaborn_boxplot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1532 <param name="color" value="blue"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1533 <param name="saturation" value="0.5"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1534 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1535 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1536 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1537 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1538 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1539 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1540 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1541 <has_text_matching expression="sc.pl.highest_expr_genes"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1542 <has_text_matching expression="n_top=30"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1543 <has_text_matching expression="gene_symbols='symbol'"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1544 <has_text_matching expression="color='blue'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1545 <has_text_matching expression="saturation=0.5"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1546 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1547 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1548 <output name="out_png" file="pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png" ftype="png" compare="image_diff"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1549 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1550
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1551 <!-- test 16 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1552 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1553 <param name="adata" value="pp.highly_variable_genes.seurat.blobs.h5ad"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1554 <param name="format" value="png"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1555 <conditional name="method">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1556 <param name="method" value="pl.highly_variable_genes"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1557 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1558 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1559 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1560 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1561 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1562 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1563 <has_text_matching expression="sc.pl.highly_variable_genes"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1564 <has_text_matching expression="adata_or_result=adata"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1565 <has_text_matching expression="log=False"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1566 <has_text_matching expression="highly_variable_genes=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1567 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1568 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1569 <output name="out_png" file="pl.highly_variable_genes.seurat.blobs.png" ftype="png" compare="image_diff"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1570 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1571
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1572 <!-- test 17 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1573 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1574 <param name="adata" value="pp.scrublet.krumsiek11.h5ad"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1575 <param name="format" value="png"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1576 <conditional name="method">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1577 <param name="method" value="pl.scrublet_score_distribution"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1578 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1579 <section name="advanced_common">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1580 <param name="show_log" value="true"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1581 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1582 <output name="hidden_output">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1583 <assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1584 <has_text_matching expression="sc.pl.scrublet_score_distribution"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1585 <has_text_matching expression="adata=adata"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1586 <has_text_matching expression="scale_hist_obs='log'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1587 <has_text_matching expression="scale_hist_sim='linear'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1588 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1589 </output>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1590 <output name="out_png" file="pl.scrublet_score_distribution.png" ftype="png" compare="image_diff"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1591 </test>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1592
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1593 <!-- test 18 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1594 <test expect_num_outputs="2">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1595 <param name="adata" value="pbmc68k_reduced.h5ad"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1596 <param name="format" value="pdf"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1597 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1598 <param name="method" value="pl.pca"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1599 <param name="color" value="CD3D,CD79A"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1600 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1601 <repeat name="components">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1602 <param name="axis1" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1603 <param name="axis2" value="2"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1604 </repeat>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1605 <repeat name="components">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1606 <param name="axis1" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1607 <param name="axis2" value="3"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1608 </repeat>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1609 <param name="legend_fontsize" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1610 <param name="legend_fontweight" value="normal"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1611 <param name="size" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1612 <param name="ncols" value="2"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1613 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1614 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1615 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1616 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1617 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1618 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1619 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1620 <has_text_matching expression="sc.pl.pca"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1621 <has_text_matching expression="save='.pdf'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1622 <has_text_matching expression="color=\['CD3D', 'CD79A'\]"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1623 <has_text_matching expression="use_raw=False"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1624 <has_text_matching expression="sort_order=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1625 <has_text_matching expression="components=\['1,2', '1,3'\]"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1626 <has_text_matching expression="projection='2d'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1627 <has_text_matching expression="legend_loc='right margin'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1628 <has_text_matching expression="legend_fontsize=1"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1629 <has_text_matching expression="legend_fontweight='normal'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1630 <has_text_matching expression="size=1.0"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1631 <has_text_matching expression="frameon=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1632 <has_text_matching expression="ncols=2"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1633 <has_text_matching expression="wspace=0.1"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1634 <has_text_matching expression="hspace=0.25"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1635 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1636 </output>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1637 <output name="out_pdf" file="pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf" ftype="pdf" compare="sim_size"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1638 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1639
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1640 <!-- test 19 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1641 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1642 <param name="adata" value="pp.pca.krumsiek11.h5ad"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1643 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1644 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1645 <param name="method" value="pl.pca_loadings"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1646 <param name="components" value="1,2,3"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1647 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1648 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1649 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1650 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1651 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1652 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1653 <has_text_matching expression="sc.pl.pca_loadings"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1654 <has_text_matching expression="components=\[1, 2, 3\]"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1655 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1656 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1657 <output name="out_png" file="pl.pca_loadings.pp.pca.krumsiek11.png" compare="image_diff"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1658 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1659
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1660 <!-- test 20 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1661 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1662 <param name="adata" value="pp.pca.krumsiek11.h5ad"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1663 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1664 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1665 <param name="method" value="pl.pca_variance_ratio"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1666 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1667 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1668 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1669 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1670 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1671 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1672 <has_text_matching expression="sc.pl.pca_variance_ratio"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1673 <has_text_matching expression="log=False"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1674 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1675 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1676 <output name="out_png" file="pl.pca_variance_ratio.pp.pca.krumsiek11.png" compare="image_diff"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1677 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1678
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1679 <!-- test 21 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1680 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1681 <param name="adata" value="pp.pca.krumsiek11.h5ad"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1682 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1683 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1684 <param name="method" value="pl.pca_overview"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1685 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1686 <param name="legend_fontsize" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1687 <param name="legend_fontweight" value="normal"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1688 <param name="size" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1689 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1690 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1691 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1692 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1693 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1694 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1695 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1696 <has_text_matching expression="sc.pl.pca_overview"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1697 <has_text_matching expression="use_raw=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1698 <has_text_matching expression="sort_order=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1699 <has_text_matching expression="projection='2d'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1700 <has_text_matching expression="legend_loc='right margin'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1701 <has_text_matching expression="legend_fontsize=1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1702 <has_text_matching expression="legend_fontweight='normal'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1703 <has_text_matching expression="size=1.0"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1704 <has_text_matching expression="frameon=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1705 <has_text_matching expression="ncols=4"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1706 <has_text_matching expression="wspace=0.1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1707 <has_text_matching expression="hspace=0.25"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1708 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1709 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1710 <output name="out_png" file="pl.pca_overview.pp.pca.krumsiek11.png" compare="image_diff"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1711 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1712
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1713 <!-- test 22 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1714 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1715 <param name="adata" value="tl.tsne.krumsiek11.h5ad"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1716 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1717 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1718 <param name="method" value="pl.tsne"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1719 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1720 <param name="legend_fontsize" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1721 <param name="legend_fontweight" value="normal"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1722 <param name="size" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1723 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1724 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1725 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1726 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1727 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1728 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1729 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1730 <has_text_matching expression="sc.pl.tsne"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1731 <has_text_matching expression="use_raw=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1732 <has_text_matching expression="edges=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1733 <has_text_matching expression="arrows=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1734 <has_text_matching expression="sort_order=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1735 <has_text_matching expression="projection='2d'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1736 <has_text_matching expression="legend_loc='right margin'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1737 <has_text_matching expression="legend_fontsize=1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1738 <has_text_matching expression="legend_fontweight='normal'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1739 <has_text_matching expression="size=1.0"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1740 <has_text_matching expression="frameon=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1741 <has_text_matching expression="ncols=4"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1742 <has_text_matching expression="wspace=0.1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1743 <has_text_matching expression="hspace=0.25"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1744 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1745 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1746 <output name="out_png" file="pl.tsne.krumsiek11.png" ftype="png" compare="image_diff"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1747 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1748
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1749 <!-- test 23 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1750 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1751 <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1752 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1753 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1754 <param name="method" value="pl.umap"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1755 <param name="color" value="paul15_clusters"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1756 <conditional name="edges">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1757 <param name="edges" value="True"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1758 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1759 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1760 <param name="legend_fontsize" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1761 <param name="legend_fontweight" value="normal"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1762 <param name="size" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1763 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1764 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1765 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1766 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1767 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1768 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1769 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1770 <has_text_matching expression="sc.pl.umap"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1771 <has_text_matching expression="color=\['paul15_clusters'\]"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1772 <has_text_matching expression="use_raw=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1773 <has_text_matching expression="edges=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1774 <has_text_matching expression="edges_width=0.1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1775 <has_text_matching expression="arrows=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1776 <has_text_matching expression="sort_order=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1777 <has_text_matching expression="projection='2d'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1778 <has_text_matching expression="legend_loc='right margin'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1779 <has_text_matching expression="legend_fontsize=1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1780 <has_text_matching expression="legend_fontweight='normal'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1781 <has_text_matching expression="size=1.0"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1782 <has_text_matching expression="frameon=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1783 <has_text_matching expression="ncols=4"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1784 <has_text_matching expression="wspace=0.1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1785 <has_text_matching expression="hspace=0.25"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1786
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1787 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1788 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1789 <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1790 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1791
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1792 <!-- test 24 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1793 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1794 <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1795 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1796 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1797 <param name="method" value="pl.diffmap"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1798 <param name="color" value="paul15_clusters"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1799 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1800 <param name="legend_fontsize" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1801 <param name="legend_fontweight" value="normal"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1802 <param name="size" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1803 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1804 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1805 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1806 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1807 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1808 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1809 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1810 <has_text_matching expression="sc.pl.diffmap"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1811 <has_text_matching expression="color=\['paul15_clusters'\]"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1812 <has_text_matching expression="use_raw=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1813 <has_text_matching expression="sort_order=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1814 <has_text_matching expression="projection='2d'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1815 <has_text_matching expression="legend_loc='right margin'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1816 <has_text_matching expression="legend_fontsize=1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1817 <has_text_matching expression="legend_fontweight='normal'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1818 <has_text_matching expression="size=1.0"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1819 <has_text_matching expression="frameon=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1820 <has_text_matching expression="ncols=4"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1821 <has_text_matching expression="wspace=0.1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1822 <has_text_matching expression="hspace=0.25"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1823
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1824 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1825 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1826 <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1827 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1828
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1829 <!-- test 25 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1830 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1831 <param name="adata" value="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1832 <param name="format" value="png"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1833 <conditional name="method">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1834 <param name="method" value="pl.draw_graph"/>
8
6adf98e782f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec"
iuc
parents: 7
diff changeset
1835 <param name="layout" value="fr"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1836 <conditional name="edges">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1837 <param name="edges" value="True"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1838 <param name="edges_color" value="Crimson"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1839 </conditional>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1840 <param name="sort_order" value="false"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1841 <section name="plot">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1842 <param name="legend_fontweight" value="normal"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1843 </section>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1844 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1845 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1846 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1847 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1848 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1849 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1850 <has_text_matching expression="sc.pl.draw_graph"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1851 <has_text_matching expression="use_raw=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1852 <has_text_matching expression="edges=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1853 <has_text_matching expression="edges_width=0.1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1854 <has_text_matching expression="edges_color='Crimson'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1855 <has_text_matching expression="arrows=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1856 <has_text_matching expression="sort_order=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1857 <has_text_matching expression="projection='2d'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1858 <has_text_matching expression="legend_loc='right margin'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1859 <has_text_matching expression="legend_fontweight='normal'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1860 <has_text_matching expression="frameon=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1861 <has_text_matching expression="ncols=4"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1862 <has_text_matching expression="wspace=0.1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1863 <has_text_matching expression="hspace=0.25"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1864 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1865 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1866 <output name="out_png" file="pl.draw_graph.png" ftype="png" compare="image_diff"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1867 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1868
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1869 <!-- test 26 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1870 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1871 <param name="adata" value="tl.embedding_density.umap.pbmc68k_reduced.h5ad"/>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1872 <param name="format" value="png"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1873 <conditional name="method">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1874 <param name="method" value="pl.embedding_density"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1875 <param name="key" value="umap_density_bulk_labels"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1876 </conditional>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1877 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1878 <param name="show_log" value="true"/>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1879 </section>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1880 <output name="hidden_output">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1881 <assert_contents>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1882 <has_text_matching expression="sc.pl.embedding_density"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1883 <has_text_matching expression="basis='umap'"/>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1884 <has_text_matching expression="key='umap_density_bulk_labels'"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1885 </assert_contents>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1886 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1887 <output name="out_png" file="pl.embedding_density.pbmc68k_reduced.png" ftype="png" compare="image_diff"/>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1888 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1889
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1890 <!-- This function is commented out because it is not compatible with pandas version. If the issue is not resolved in the next update, this should be removed. -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1891 <!-- test 27 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1892 <!-- <test expect_num_outputs="2">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1893 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1894 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1895 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1896 <param name="method" value="pl.dpt_groups_pseudotime"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1897
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1898 </conditional>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1899 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1900 <param name="show_log" value="true"/>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1901 </section>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1902 <output name="hidden_output">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1903 <assert_contents>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1904 <has_text_matching expression="sc.pl.dpt_groups_pseudotime"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1905 <has_text_matching expression="color_map='viridis'"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1906 </assert_contents>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1907 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1908 <output name="out_png" file="pl.dpt_groups_pseudotime.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1909 </test> -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1910
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1911 <!-- test 28 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1912 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1913 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1914 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1915 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1916 <param name="method" value="pl.dpt_timeseries"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1917 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1918 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1919 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1920 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1921 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1922 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1923 <has_text_matching expression="sc.pl.dpt_timeseries"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1924 <has_text_matching expression="as_heatmap=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1925 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1926 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1927 <output name="out_png" file="pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1928 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1929
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1930 <!-- test 29 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1931 <test expect_num_outputs="1">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1932 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1933 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1934 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1935 <param name="method" value="pl.paga"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1936 <param name="threshold" value="0.01"/>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1937 <param name="color" value="louvain"/>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1938 <param name="layout" value="fr"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1939 <param name="fontsize" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1940 <param name="edge_width_scale" value="5"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1941 </conditional>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1942 <output name="out_png" file="pl.paga.paul15_gauss_braycurtis.png" ftype="png" compare="image_diff"/>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1943 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1944
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1945 <!-- test 30 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1946 <test expect_num_outputs="1">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1947 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad"/>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1948 <param name="format" value="png"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1949 <conditional name="method">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1950 <param name="method" value="pl.paga_compare"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1951 <param name="threshold" value="0.01"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1952 <param name="color" value="louvain"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1953 <param name="layout" value="fr"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1954 <param name="fontsize" value="1"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1955 <param name="edge_width_scale" value="5"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1956 </conditional>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1957 <output name="out_png" file="pl.paga_compare.paul15_gauss_braycurtis.png" ftype="png" compare="image_diff"/>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1958 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1959
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1960 <!-- test 31 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1961 <!-- <test expect_num_outputs="2">
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1962 test pl.paga_path
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1963 </test> -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1964
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1965 <!-- test 32 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1966 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1967 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1968 <param name="format" value="png"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1969 <conditional name="method">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1970 <param name="method" value="pl.rank_genes_groups"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1971 <param name="n_genes" value="10"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1972 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1973 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1974 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1975 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1976 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1977 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1978 <has_text_matching expression="sc.pl.rank_genes_groups"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1979 <has_text_matching expression="n_genes=10"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1980 <has_text_matching expression="fontsize=8"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1981 <has_text_matching expression="ncols=4"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1982 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1983 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1984 <output name="out_png" file="pl.rank_genes_groups.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1985 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1986
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1987 <!-- test 33 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1988 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1989 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1990 <param name="format" value="png"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1991 <conditional name="method">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1992 <param name="method" value="pl.rank_genes_groups_violin"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1993 <conditional name="genes">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1994 <param name="select" value="n_genes"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1995 <param name="n_genes" value="10"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1996 </conditional>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1997 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1998 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1999 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2000 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2001 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2002 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2003 <has_text_matching expression="sc.pl.rank_genes_groups_violin"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2004 <has_text_matching expression="n_genes=10"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2005 <has_text_matching expression="use_raw=None"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2006 <has_text_matching expression="split=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2007 <has_text_matching expression="strip=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2008 <has_text_matching expression="jitter=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2009 <has_text_matching expression="size=1"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2010 <has_text_matching expression="density_norm='width'"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2011 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2012 </output>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2013 <output_collection name="collection_png">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2014 <element name="cell_type_Ery" file="pl.rank_genes_groups_violin.Ery.png" ftype="png" compare="image_diff" eps="3.5"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2015 <element name="cell_type_Mk" file="pl.rank_genes_groups_violin.Mk.png" ftype="png" compare="image_diff" eps="3.5"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2016 <element name="cell_type_Mo" file="pl.rank_genes_groups_violin.Mo.png" ftype="png" compare="image_diff" eps="3.5"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2017 <element name="cell_type_Neu" file="pl.rank_genes_groups_violin.Neu.png" ftype="png" compare="image_diff" eps="3.5"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2018 <element name="cell_type_progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="image_diff" eps="3.5"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2019 </output_collection>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2020 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2021
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2022 <!-- test 34 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
2023 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2024 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2025 <param name="format" value="png"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2026 <conditional name="method">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2027 <param name="method" value="pl.rank_genes_groups_stacked_violin"/>
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2028 <param name="n_genes" value="10"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2029 <param name="dendrogram" value="True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2030 <param name="swap_axes" value="True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2031 <section name="violin_plot">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2032 <conditional name="stripplot">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2033 <param name="size" value="1"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2034 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2035 <param name="density_norm" value="width"/>
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2036 </section>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2037 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2038 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2039 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2040 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2041 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2042 <assert_contents>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2043 <has_text_matching expression="sc.pl.rank_genes_groups_stacked_violin"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2044 <has_text_matching expression="n_genes=10"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2045 <has_text_matching expression="log=False"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2046 <has_text_matching expression="use_raw=None"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2047 <has_text_matching expression="dendrogram=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2048 <has_text_matching expression="swap_axes=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2049 <has_text_matching expression="stripplot=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2050 <has_text_matching expression="jitter=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2051 <has_text_matching expression="size=1"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2052 <has_text_matching expression="density_norm='width'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2053 <has_text_matching expression="bw_method='scott'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2054 <has_text_matching expression="saturation=0.75"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2055 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2056 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2057 <output name="out_png" file="pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff" eps="1.5"/>
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2058 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2059
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2060 <!-- test 35 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
2061 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2062 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2063 <param name="format" value="png"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2064 <conditional name="method">
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2065 <param name="method" value="pl.rank_genes_groups_heatmap"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2066 <param name="n_genes" value="10"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2067 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2068 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2069 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2070 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2071 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2072 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2073 <has_text_matching expression="sc.pl.rank_genes_groups_heatmap"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2074 <has_text_matching expression="n_genes=10"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2075 <has_text_matching expression="log=False"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2076 <has_text_matching expression="use_raw=None"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2077 <has_text_matching expression="dendrogram=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2078 <has_text_matching expression="swap_axes=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2079 <has_text_matching expression="show_gene_labels=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2080 <has_text_matching expression="origin='upper'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2081 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2082 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2083 <output name="out_png" file="pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/>
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2084 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2085
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2086 <!-- test 36 -->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
2087 <test expect_num_outputs="2">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2088 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2089 <param name="format" value="png"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2090 <conditional name="method">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2091 <param name="method" value="pl.rank_genes_groups_dotplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2092 <param name="n_genes" value="10"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2093 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2094 <section name="advanced_common">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2095 <param name="show_log" value="true"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2096 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2097 <output name="hidden_output">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2098 <assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2099 <has_text_matching expression="sc.pl.rank_genes_groups_dotplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2100 <has_text_matching expression="n_genes=10"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2101 <has_text_matching expression="log=False"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2102 <has_text_matching expression="use_raw=None"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2103 <has_text_matching expression="dendrogram=False"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2104 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2105 </output>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2106 <output name="out_png" file="pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2107 </test>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2108
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2109 <!-- test 37 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2110 <test expect_num_outputs="2">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2111 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2112 <param name="format" value="png"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2113 <conditional name="method">
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2114 <param name="method" value="pl.rank_genes_groups_matrixplot"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2115 <param name="n_genes" value="10"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2116 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2117 <section name="advanced_common">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2118 <param name="show_log" value="true"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2119 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2120 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2121 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2122 <has_text_matching expression="sc.pl.rank_genes_groups_matrixplot"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2123 <has_text_matching expression="n_genes=10"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2124 <has_text_matching expression="log=False"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2125 <has_text_matching expression="use_raw=None"/>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2126 <has_text_matching expression="dendrogram=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2127 <has_text_matching expression="swap_axes=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2128 <has_text_matching expression="snap=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2129 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2130 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2131 <output name="out_png" file="pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/>
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2132 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2133
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2134 <!-- test 38 pl.rank_genes_groups_dotplot with marker list-->
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
2135 <test expect_num_outputs="2">
16
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2136 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" />
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2137 <param name="format" value="png"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2138 <conditional name="method">
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2139 <param name="method" value="pl.rank_genes_groups_dotplot"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2140 <conditional name="var_names">
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2141 <param name="type" value="customfile"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2142 <param name="var_names" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.tsv"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2143 </conditional>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2144 </conditional>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2145 <section name="advanced_common">
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2146 <param name="show_log" value="true" />
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2147 </section>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2148 <output name="hidden_output">
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2149 <assert_contents>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2150 <has_text_matching expression="sc.pl.rank_genes_groups_dotplot"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2151 <has_text_matching expression="log=False"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2152 <has_text_matching expression="use_raw=None"/>
16
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2153 <has_text_matching expression="dendrogram=False"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2154 </assert_contents>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2155 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2156 <output name="out_png" file="pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.png" ftype="png" compare="image_diff"/>
16
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2157 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2158
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2159 <!-- test 39: pl.rank_genes_groups_dotplot with marker list -->
16
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2160 <test expect_num_outputs="2">
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2161 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" />
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2162 <param name="format" value="png"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2163 <conditional name="method">
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2164 <param name="method" value="pl.rank_genes_groups_dotplot"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2165 <conditional name="var_names">
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2166 <param name="type" value="customfile"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2167 <param name="var_names" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.tsv"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2168 </conditional>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2169 </conditional>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2170 <section name="advanced_common">
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2171 <param name="show_log" value="true" />
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2172 </section>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2173 <output name="hidden_output">
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2174 <assert_contents>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2175 <has_text_matching expression="sc.pl.rank_genes_groups_dotplot"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2176 <has_text_matching expression="log=False"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2177 <has_text_matching expression="use_raw=None"/>
16
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2178 <has_text_matching expression="dendrogram=False"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2179 </assert_contents>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2180 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2181 <output name="out_png" file="pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.png" ftype="png" compare="image_diff"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2182 </test>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2183
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2184 <!-- test 40 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2185 <test expect_num_outputs="2">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2186 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" />
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2187 <param name="format" value="png"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2188 <conditional name="method">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2189 <param name="method" value="pl.rank_genes_groups_tracksplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2190 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2191 <section name="advanced_common">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2192 <param name="show_log" value="true" />
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2193 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2194 <output name="hidden_output">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2195 <assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2196 <has_text_matching expression="sc.pl.rank_genes_groups_tracksplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2197 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2198 </output>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2199 <output name="out_png" file="pl.rank_genes_groups_tracksplot.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.png" ftype="png" compare="image_diff"/>
16
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2200 </test>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2201 </tests>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2202 <help><![CDATA[
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2203 Generic: Scatter plot along observations or variables axes (`pl.scatter`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2204 =========================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2205
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2206 Color the plot using annotations of observations (`.obs`), variables
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2207 (`.var`) or expression of genes (`.var_names`).
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2208
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2209 More details on the `scanpy documentation
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
2210 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.scatter.html>`__
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2211
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2212 Generic: Heatmap of the expression values of set of genes (`pl.heatmap`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2213 ========================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2214
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2215 If `groupby` is given, the heatmap is ordered by the respective group. For
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2216 example, a list of marker genes can be plotted, ordered by clustering. If
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2217 the `groupby` observation annotation is not categorical the observation
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2218 annotation is turned into a categorical by binning the data into the number
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2219 specified in `num_categories`.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2220
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2221 More details on the `scanpy documentation
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
2222 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.heatmap.html>`__
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2223
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2224 Generic: Makes a dot plot of the expression values (`pl.dotplot`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2225 =================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2226
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2227 For each var_name and each `groupby` category a dot is plotted. Each dot
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2228 represents two values: mean expression within each category (visualized by
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2229 color) and fraction of cells expressing the var_name in the
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2230 category. (visualized by the size of the dot). If groupby is not given, the
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2231 dotplot assumes that all data belongs to a single category. A gene is not
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2232 considered expressed if the expression value in the adata (or adata.raw) is
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2233 equal to zero.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2234
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2235 For instance, for each marker gene, the mean value and the percentage of cells
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2236 expressing the gene can be visualized for each cluster.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2237
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2238 More details on the `scanpy documentation
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
2239 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.dotplot.html>`__
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2240
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2241 Generic: Tracks plot (`pl.tracksplot`)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2242 ======================================
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2243
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2244 In this type of plot each var_name is plotted as a filled line plot where the y values correspond to the var_name values and x is each of the cells.
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2245 Best results are obtained when using raw counts that are not log.
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2246
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2247 More details on the `scanpy documentation
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2248 <https://scanpy.readthedocs.io/en/stable/generated/scanpy.pl.tracksplot.html>`__
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2249
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2250 Generic: Violin plot (`pl.violin`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2251 ==================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2252
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2253 Wraps `seaborn.violinplot` for `anndata.AnnData`.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2254
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2255 More details on the `scanpy documentation
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
2256 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.violin.html>`__
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2257
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2258 Generic: Stacked violin plots (`pl.stacked_violin`)
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2259 ===================================================
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2260
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2261 Makes a compact image composed of individual violin plots (from `seaborn.violinplot`)
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2262 stacked on top of each other. Useful to visualize gene expression per cluster.
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2263
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2264 More details on the `scanpy documentation
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
2265 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.stacked_violin.html>`__
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2266
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2267 Generic: Heatmap of the mean expression values per cluster (`pl.matrixplot`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2268 ============================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2269
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2270 Creates a heatmap of the mean expression values per cluster of each var_names
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2271
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2272 If groupby is not given, the matrixplot assumes that all data belongs to a single
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2273 category.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2274
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2275 More details on the `scanpy documentation
14
f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
2276 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.matrixplot.html>`__
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2277
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2278 Generic: Hierarchically-clustered heatmap (`pl.clustermap`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2279 ===========================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2280
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2281 Wraps `seaborn.clustermap
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2282 <https://seaborn.pydata.org/generated/seaborn.clustermap.html>`__ for
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2283 `anndata.AnnData`.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2284
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2285 The returned object has a savefig() method that should be used if you want
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2286 to save the figure object without clipping the dendrograms.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2287
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2288 To access the reordered row indices, use:
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2289 clustergrid.dendrogram_row.reordered_ind
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2290
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2291 Column indices, use: clustergrid.dendrogram_col.reordered_ind
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2292
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2293 More details on the `scanpy documentation
14
f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
2294 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.clustermap.html>`__
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2295
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2296 Preprocessing: Plot the fraction of counts assigned to each gene over all cells (`pl.highest_expr_genes`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2297 =========================================================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2298
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2299 Computes, for each gene, the fraction of counts assigned to that gene within
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2300 a cell. The `n_top` genes with the highest mean fraction over all cells are
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2301 plotted as boxplots.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2302
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2303 This plot is similar to the `scater` package function `plotHighestExprs(type= "highest-expression")`
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2304
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2305 More details on the `scanpy documentation
14
f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
2306 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.highest_expr_genes.html>`__
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2307
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2308 Preprocessing: Plot dispersions versus means for genes (`pl.highly_variable_genes`)
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2309 ===================================================================================
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2310
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2311 It produces Supp. Fig. 5c of Zheng et al. (2017) and MeanVarPlot() of Seurat.
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2312
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2313 More details on the `scanpy documentation
14
f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
2314 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.highly_variable_genes.html>`__
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2315
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2316 Preprocessing: Plot histogram of doublet scores for observed transcriptomes and simulated doublets (`pl.scrublet_score_distribution`)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2317 =====================================================================================================================================
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2318
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2319 The histogram for simulated doublets is useful for determining the correct doublet score threshold.
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2320 Scrublet must have been run previously with the input object.
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2321
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2322 More details on the `scanpy documentation
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2323 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.scrublet_score_distribution.html>`__
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2324
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2325 PCA: Scatter plot in PCA coordinates (`pl.pca`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2326 ===============================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2327
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2328 More details on the `scanpy documentation
14
f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
2329 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca.html>`__
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2330
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2331 PCA: Rank genes according to contributions to PCs (`pl.pca_loadings`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2332 =====================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2333
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2334 More details on the `scanpy documentation
14
f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
2335 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca_loadings.html>`__
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2336
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2337 PCA: Plot the variance ratio (`pl.pca_variance_ratio`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2338 ======================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2339
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2340 More details on the `scanpy documentation
14
f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
2341 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca_variance_ratio.html>`__
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2342
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2343 PCA: Plot PCA results (`pl.pca_overview`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2344 =========================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2345
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2346 The parameters are the ones of the scatter plot. Call pca_ranking separately
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2347 if you want to change the default settings.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2348
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2349 More details on the `scanpy documentation
14
f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
2350 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca_overview.html>`__
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2351
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2352 Embedding: Scatter plot in tSNE basis (`pl.tsne`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2353 =================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2354
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2355 More details on the `scanpy documentation
14
f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
2356 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.tsne.html>`__
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2357
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2358 Embeddings: Scatter plot in UMAP basis (`pl.umap`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2359 ==================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2360
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2361 More details on the `scanpy documentation
14
f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
2362 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.umap.html>`__
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2363
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2364 Embeddings: Scatter plot in Diffusion Map basis (`pl.diffmap`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2365 ==============================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2366
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2367 More details on the `scanpy documentation
14
f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
2368 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.diffmap.html>`__
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2369
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2370 Embeddings: Scatter plot in graph-drawing basis (`pl.draw_graph`)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2371 =================================================================
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2372
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2373 More details on the `scanpy documentation
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2374 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.draw_graph.html>`__
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2375
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2376 Embeddings: Plot the density of cells in an embedding (per condition) (`pl.embedding_density`)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2377 ==============================================================================================
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2378
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2379 More details on the `scanpy documentation
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2380 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.embedding_density.html>`__
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2381
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2382 .. This function is commented out because it is not compatible with pandas version. If the issue is not resolved in the next update, this should be removed.
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2383 .. Branching trajectories and pseudotime, clustering: Plot groups and pseudotime (`pl.dpt_groups_pseudotime`)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2384 .. ===========================================================================================================
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2385
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2386 .. More details on the `scanpy documentation
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2387 .. <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.dpt_groups_pseudotime.html>`__
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2388
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2389 Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series (`pl.dpt_timeseries`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2390 =====================================================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2391
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2392 More details on the `scanpy documentation
14
f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
2393 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.dpt_timeseries.html>`__
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2394
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2395
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2396 Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges (`pl.paga`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2397 ====================================================================================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2398
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2399 This uses ForceAtlas2 or igraph's layout algorithms for most layouts.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2400
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2401 When initializing the positions, note that - for some reason - igraph
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2402 mirrors coordinates along the x axis... that is, you should increase the
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2403 `maxiter` parameter by 1 if the layout is flipped.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2404
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2405 More details on the `scanpy documentation
14
f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
2406 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.paga.html>`__
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2407
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2408
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2409 Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side (`pl.paga_compare`)
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2410 ==========================================================================================================
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2411
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2412 More details on the `scanpy documentation
14
f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
2413 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.paga_compare.html>`__
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2414
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2415 Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths (`pl.paga_path`)
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2416 ======================================================================================================================
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2417
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2418 More details on the `scanpy documentation
14
f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
2419 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.paga_path.html>`__
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2420
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2421 Marker genes: Plot ranking of genes using dotplot plot (`pl.rank_genes_groups`)
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2422 ===============================================================================
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2423
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2424 More details on the `scanpy documentation
14
f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
2425 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups.html>`__
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2426
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2427 Marker genes: Plot ranking of genes as violin plot (`pl.rank_genes_groups_violin`)
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2428 ==================================================================================
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2429
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2430 More details on the `scanpy documentation
14
f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
2431 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_violin.html>`__
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2432
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2433 Marker genes: Plot ranking of genes as stacked violin plot (`pl.rank_genes_groups_stacked_violin`)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2434 ==================================================================================================
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2435
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2436 More details on the `scanpy documentation
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2437 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_stacked_violin.html>`__
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2438
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2439 Marker genes: Plot ranking of genes as heatmap plot (`pl.rank_genes_groups_heatmap`)
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2440 ====================================================================================
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2441
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2442 More details on the `scanpy documentation
14
f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
2443 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_heatmap.html>`__
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2444
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2445 Marker genes: Plot ranking of genes as dotplot plot (`pl.rank_genes_groups_dotplot`)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2446 ====================================================================================
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2447
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2448 More details on the `scanpy documentation
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2449 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_dotplot.html>`__
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2450
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2451 Marker genes: Plot ranking of genes as matrixplot plot (`pl.rank_genes_groups_matrixplot`)
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2452 ==========================================================================================
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2453
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2454 More details on the `scanpy documentation
14
f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
2455 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_matrixplot.html>`__
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2456
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2457 ]]>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2458 </help>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2459 <expand macro="citations"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2460 </tool>