Mercurial > repos > iuc > scanpy_plot

annotate plot.xml @ 19:40812a65a78b draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
author iuc
date Thu, 03 Oct 2024 22:44:36 +0000
parents 2dfb2227a16c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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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@">
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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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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
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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
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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='$method.type.x'
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
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parents: 10
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29 y_field='$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
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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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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
iuc
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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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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46 #end if
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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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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':
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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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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
parents: 16
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53 #if str($method.type.color) != '':
7
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
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54 color='$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
parents: 16
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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=$method.sort_order,
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2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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68 @CMD_PARAM_GROUPS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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69 @CMD_PARAM_PL_COMPONENTS@
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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70 projection='$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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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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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',
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40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
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78 #end if
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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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'],
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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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81 #end if
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82 frameon=$method.plot.frameon,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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83 @CMD_PARAM_SIZE@
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84 @CMD_PARAM_TITLE@
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85 @CMD_SHOW_NONE@)
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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86
17
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diff changeset
87 #else if str($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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diff changeset
90 @CMD_PARAM_PLOT_INPUTS@
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parents: 16
diff changeset
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@
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iuc
parents: 16
diff changeset
94 @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
95 @CMD_SHOW_NONE@)
0
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96
17
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diff changeset
97 #else if str($method.method) == 'pl.dotplot':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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98 @CMD_VAR_NAMES_HEADER_CHECK@
0
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99 sc.pl.dotplot(
17
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100 @CMD_PARAM_PLOT_INPUTS@
19
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101 @CMD_PARAMS_INPUTS@
17
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102 @CMD_PARAM_GENE_SYMBOLS@
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103 @CMD_PARAMS_PLOTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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104 @CMD_PL_DOTPLOT@
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parents: 16
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105 @CMD_SHOW_NONE@)
0
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106
17
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107 #else if str($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@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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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='$method.groupby',
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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129 #end if
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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130 log=$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=$method.rotation,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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142 #end if
17
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143 @CMD_PARAMS_SEABORN_VIOLINPLOT@
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144 @CMD_PARAM_LAYER@
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145 @CMD_SHOW_NONE@)
0
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146
17
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147 #else if str($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($method.method) == 'pl.matrixplot':
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158 @CMD_VAR_NAMES_HEADER_CHECK@
0
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159 sc.pl.matrixplot(
17
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160 @CMD_PARAM_PLOT_INPUTS@
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diff changeset
161 @CMD_PARAMS_INPUTS@
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iuc
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diff changeset
162 @CMD_PARAM_GENE_SYMBOLS@
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iuc
parents: 16
diff changeset
163 @CMD_PARAMS_PLOTS@
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iuc
parents: 16
diff changeset
164 @CMD_PARAMS_PL_MATRIXPLOT@
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165 @CMD_SHOW_NONE@)
0
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166
17
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diff changeset
167 #else if str($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
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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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,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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178 method='$method.seaborn_clustermap.method',
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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179 metric='$method.seaborn_clustermap.metric',
17
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180 #if str($method.seaborn_clustermap.z_score) != 'None':
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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181 z_score=$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($method.seaborn_clustermap.standard_scale) != 'None':
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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184 standard_scale=$method.seaborn_clustermap.standard_scale,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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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
iuc
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188 save='.$format',
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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189 @CMD_SHOW_NONE@)
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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190
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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diff changeset
191 #else if str($method.method) == 'pl.highest_expr_genes':
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
192 sc.pl.highest_expr_genes(
17
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193 @CMD_PARAM_PLOT_INPUTS@
0
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194 n_top=$method.n_top,
17
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195 @CMD_PARAM_GENE_SYMBOLS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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196 #if str($method.setseaborn_boxplot.color) != '':
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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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 $method.setseaborn_boxplot.palette:
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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200 palette='$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=$method.setseaborn_boxplot.saturation,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
203 @CMD_SHOW_NONE@)
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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204
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 16
diff changeset
205 #else if str($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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diff changeset
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
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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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iuc
parents: 16
diff changeset
219 save='.$format',
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
220 @CMD_SHOW_NONE@)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
221
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
222 #else if str($method.method) == 'pl.pca':
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
223 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
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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diff changeset
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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diff changeset
230 @CMD_SCATTER_OUTINE@
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iuc
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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
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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234
17
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diff changeset
235 #else if str($method.method) == 'pl.pca_loadings':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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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(',')])
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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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($method.n_points) != '':
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diff changeset
242 n_points=$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
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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diff changeset
244 @CMD_SHOW_NONE@)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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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($method.method) == 'pl.pca_variance_ratio':
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
247 sc.pl.pca_variance_ratio(
17
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248 @CMD_PARAM_PLOT_INPUTS@
0
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parents:
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249 n_pcs=$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@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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@
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
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diff changeset
262 @CMD_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
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@
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
277 @CMD_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
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
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
369 @CMD_ANNDATA_WRITE_OUTPUTS@
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
370
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
371 #else if str($method.method) == 'pl.paga_compare':
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
372 sc.pl.paga_compare(
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
373 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
374 @CMD_PARAMS_PL_PAGA@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
375 @CMD_PARAM_PL_COMPONENTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
376 projection='$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
377 #if str($method.plot.legend_loc) != '':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
378 legend_loc='$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
379 #end if
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
380 @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
381 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
382 #if $method.plot.color_map:
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
383 color_map='$method.plot.color_map',
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
384 #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
385 #if $method.plot.palette:
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
386 palette=['$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
387 #end if
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
388 @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
389 @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
390 @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
391
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
392 #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
393 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
394 @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
395 #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
396 nodes=$nodes,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
397 #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
398 keys=$keys,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
399 use_raw=$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
400 #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
401 #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
402 annotations=$annotations,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
403 #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
404 #if $method.color_map:
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
405 color_map='$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
406 #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
407 n_avg=$method.n_avg,
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
408 #if str($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
409 groups_key='$method.groups_key',
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
410 #end if
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
411 as_heatmap=$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
412 show_node_names=$method.show_node_names,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
413 show_colorbar=$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
414 show_yticks=$method.show_yticks,
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
415 normalize_to_zero_one=$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
416 @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
417
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
418 #else if str($method.method) == 'pl.rank_genes_groups':
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
419 sc.pl.rank_genes_groups(
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
420 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
421 @CMD_PARAM_GROUPS@
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
422 n_genes=$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
423 @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
424 fontsize=$method.fontsize,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
425 ncols=$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
426 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
427 @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
428
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
429 #else if $method.method == 'pl.rank_genes_groups_violin'
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
430 sc.pl.rank_genes_groups_violin(
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
431 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
432 @CMD_PARAM_GROUPS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
433 #if str($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
434 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
435 #else
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
436 #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
437 gene_names=$gene_names,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
438 #end if
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
439 @CMD_PARAM_GENE_SYMBOLS@
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
440 use_raw=$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
441 split=$method.split,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
442 strip=$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
443 #if str($method.violin_plot.stripplot.stripplot) == 'True':
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
444 jitter=$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
445 #if str($method.violin_plot.stripplot.jitter.jitter) == 'True':
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
446 size=$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
447 #end if
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
448 #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
449 density_norm='$method.violin_plot.density_norm',
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
450 @CMD_SHOW_NONE@)
16
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
451
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
452 #else if str($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
453 @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
454 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
455 @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
456 @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
457 @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
458 @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
459 @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
460 @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
461
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
462 #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
463 @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
464 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
465 @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
466 @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
467 @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
468 @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
469 @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
470 @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
471
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
472 #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
473 @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
474 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
475 @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
476 @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
477 @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
478 @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
479 @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
480 @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
481 @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
482
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
483 #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
484 @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
485 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
486 @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
487 @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
488 @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
489 @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
490 @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
491 @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
492 @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
493
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
494 #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
495 @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
496 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
497 @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
498 @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
499 @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
500 @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
501 @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
502 @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
503
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
504 #end if
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
505 ]]></configfile>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
506 </configfiles>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
507 <inputs>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
508 <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
509 <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
510 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
511 <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
512 <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
513 <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
514 <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
515 <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
516 <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
517 <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
518 <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
519 <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
520 <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
521 <option value="pl.highly_variable_genes">Preprocessing: Plot dispersions versus means for genes, using 'pl.highly_variable_genes'</option>
17
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diff changeset
522 <option value="pl.scrublet_score_distribution">Preprocessing: Plot histogram of doublet scores, using 'pl.scrublet_score_distribution'</option>
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parents: 2
diff changeset
523 <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"
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parents: 2
diff changeset
524 <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
525 <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
526 <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"
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parents: 2
diff changeset
527 <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"
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parents: 2
diff changeset
528 <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"
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parents: 2
diff changeset
529 <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
530 <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
531 <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
532 <!-- 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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parents: 16
diff changeset
533 <!-- <option value="pl.dpt_groups_pseudotime">Branching trajectories and pseudotime, clustering: Plot groups and pseudotime, using 'pl.dpt_groups_pseudotime'</option> -->
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parents: 2
diff changeset
534 <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
535 <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
536 <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
537 <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
538 <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
539 <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
540 <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>
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parents: 2
diff changeset
541 <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
542 <option value="pl.rank_genes_groups_dotplot">Marker genes: Plot ranking of genes as dotplot plot, using 'pl.rank_genes_groups_dotplot'</option>
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parents: 2
diff changeset
543 <option value="pl.rank_genes_groups_matrixplot">Marker genes: Plot ranking of genes as matrixplot plot, using 'pl.rank_genes_groups_matrixplot'</option>
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parents: 16
diff changeset
544 <option value="pl.rank_genes_groups_tracksplot">Marker genes: Plot ranking of genes as tracksplot plot, using 'pl.rank_genes_groups_tracksplot'</option>
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545 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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546 <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
547 <conditional name="type">
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548 <param name="type" type="select" label="Plotting tool that computed coordinates">
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parents: 16
diff changeset
549 <option value="xy" selected="true">Using coordinates</option>
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diff changeset
550 <option value="basis">Using tool that computes coordinates</option>
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diff changeset
551 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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552 <when value="xy">
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parents: 6
diff changeset
553 <param argument="x" type="text" value="" label="x coordinate" help="Index or key from either '.obs' or '.var'">
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diff changeset
554 <expand macro="sanitize_query"/>
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555 </param>
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diff changeset
556 <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
557 <expand macro="sanitize_query"/>
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diff changeset
558 </param>
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parents: 10
diff changeset
559 <expand macro="param_log"/>
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parents: 6
diff changeset
560 <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
561 <expand macro="sanitize_query"/>
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diff changeset
562 </param>
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parents: 0
diff changeset
563 <conditional name="layers">
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
564 <param argument="use_layers" type="select" label="Use the layers attribute?">
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diff changeset
565 <option value="false" selected="true">No</option>
1
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parents: 0
diff changeset
566 <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
567 </param>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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568 <when value="true">
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diff changeset
569 <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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570 <expand macro="sanitize_query"/>
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diff changeset
571 </param>
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diff changeset
572 <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
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573 <expand macro="sanitize_query"/>
7
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diff changeset
574 </param>
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parents: 6
diff changeset
575 <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
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576 <expand macro="sanitize_query"/>
7
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577 </param>
1
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parents: 0
diff changeset
578 </when>
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parents: 0
diff changeset
579 <when value="false"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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580 </conditional>
0
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581 </when>
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582 <when value="basis">
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parents: 16
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583 <param argument="basis" type="select" label="Plotting tool that computes coordinates">
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584 <option value="pca">pca (need to run on 'pl.pca' output)</option>
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parents: 2
diff changeset
585 <option value="tsne">tsne (need to run on 'tl.tsne' output)</option>
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parents: 2
diff changeset
586 <option value="umap">umap (need to run on 'tl.umap' output)</option>
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parents: 2
diff changeset
587 <option value="diffmap">diffmap (need to run on 'tl.diffmap' output)</option>
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parents: 2
diff changeset
588 <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
589 </param>
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parents:
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590 <expand macro="param_color"/>
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diff changeset
591 </when>
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592 </conditional>
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parents: 16
diff changeset
593 <expand macro="param_use_raw" falsevalue="None"/>
0
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594 <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
595 <expand macro="param_groups"/>
0
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596 <section name="plot" title="Plot attributes">
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diff changeset
597 <expand macro="param_pl_components"/>
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598 <expand macro="param_projection"/>
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diff changeset
599 <expand macro="param_legend_loc"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
600 <expand macro="param_legend_fontsize"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
601 <expand macro="param_legend_fontweight"/>
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_color_map"/>
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_palette"/>
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_frameon"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
605 <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
606 <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
607 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
608 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
609 <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
610 <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
611 <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
612 <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
613 <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
614 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
615 <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
616 <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
617 <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
618 <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
619 <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
620 </when>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
621 <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
622 <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
623 <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
624 <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
625 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
626 <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
627 <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
628 <param name="type" type="select" label="Keys for accessing variables">
17
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iuc
parents: 16
diff changeset
629 <option value="var_names" selected="true">All variables in '.var_names'</option>
3
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iuc
parents: 2
diff changeset
630 <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
631 <option value="custom">Subset of variables in 'adata.var_names' or fields of '.obs'</option>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
632 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
633 <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
634 <when value="obs"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
635 <when value="custom">
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 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
637 <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
638 </param>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
639 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
640 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
641 <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
642 <expand macro="param_log"/>
17
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iuc
parents: 16
diff changeset
643 <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
644 <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
645 <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
646 <conditional name="multi_panel">
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
647 <param argument="multi_panel" type="select" label="Display keys in multiple panels" help="Also when 'groupby is not provided">
19
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iuc
parents: 17
diff changeset
648 <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
649 <option value="True">Yes</option>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
650 </param>
17
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iuc
parents: 16
diff changeset
651 <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
652 <when value="True">
17
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iuc
parents: 16
diff changeset
653 <!-- <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
654 <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
655 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
656 </conditional>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
657 </section>
7
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iuc
parents: 6
diff changeset
658 <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
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
659 <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
660 </param>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
661 <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
662 <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
663 <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
664 </when>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
665 <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
666 <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
667 <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
668 <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
669 <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
670 </when>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
671 <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
672 <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
673 <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
674 <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
675 <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
676 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
677 <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
678 <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
679 <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
680 </param>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
681 <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
682 <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
683 <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
684 <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
685 <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
686 <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
687 <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
688 <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
689 <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
690 <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
691 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
692 <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
693 <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
694 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
695 <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
696 <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
697 <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
698 <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
699 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
700 <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
701 <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
702 <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
703 <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
704 </param>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
705 <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
706 <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
707 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
708 </when>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
709 <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
710 <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
711 <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
712 <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
713 <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
714 <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
715 <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
716 </param>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
717 <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
718 <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
719 </param>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
720 <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
721 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
722 </when>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
723 <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
724 <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
725 <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
726 </when>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
727 <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
728 <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
729 <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
730 <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
731 <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
732 <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
733 </param>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
734 <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
735 <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
736 <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
737 <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
738 <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
739 </param>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
740 <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
741 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
742 <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
743 <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
744 <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
745 <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
746 <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
747 <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
748 <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
749 <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
750 <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
751 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
752 <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
753 <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
754 <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
755 </param>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
756 <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
757 <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
758 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
759 <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
760 <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
761 <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
762 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
763 <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
764 <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
765 <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
766 <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
767 <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
768 <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
769 <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
770 <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
771 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
772 <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
773 <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
774 <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
775 <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
776 <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
777 <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
778 <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
779 <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
780 <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
781 <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
782 <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
783 <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
784 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
785 <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
786 <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
787 <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
788 <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
789 <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
790 <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
791 <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
792 <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
793 <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
794 <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
795 <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
796 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
797 <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
798 <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
799 <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
800 <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
801 <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
802 <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
803 <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
804 <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
805 <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
806 </when>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
807 <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
808 <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
809 <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
810 <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
811 <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
812 <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
813 </param>
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="pl_edges"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
815 <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
816 <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
817 <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
818 <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
819 <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
820 <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
821 <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
822 </when>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
823 <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
824 <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
825 <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
826 </param>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
827 <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
828 <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
829 </param>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
830 <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
831 <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
832 </param>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
833 <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
834 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
835 <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
836 </param>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
837 <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
838 <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
839 <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
840 <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
841 <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
842 <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
843 </when>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
844 <!-- 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
845 <!-- <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
846 <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
847 </when> -->
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
848 <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
849 <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
850 <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
851 <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
852 <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
853 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
854 <when value="True">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
855 <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
856 </when>
17
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iuc
parents: 16
diff changeset
857 <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
858 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
859 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
860 <when value="pl.paga">
17
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iuc
parents: 16
diff changeset
861 <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
862 </when>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
863 <when value="pl.paga_compare">
17
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iuc
parents: 16
diff changeset
864 <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
865 <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
866 <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
867 <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
868 <expand macro="param_legend_loc">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
869 <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
870 <option value="right margin">right margin</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
871 </expand>
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_legend_fontsize"/>
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_legend_fontweight"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
874 <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
875 <expand macro="param_palette"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
876 <expand macro="param_frameon"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
877 <expand macro="param_size"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
878 <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
879 </section>
1
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iuc
parents: 0
diff changeset
880 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
881 <when value="pl.paga_path">
17
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parents: 16
diff changeset
882 <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
883 <expand macro="sanitize_query"/>
7
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iuc
parents: 6
diff changeset
884 </param>
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parents: 6
diff changeset
885 <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
886 <expand macro="sanitize_query"/>
7
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parents: 6
diff changeset
887 </param>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
888 <expand macro="param_use_raw"/>
17
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parents: 16
diff changeset
889 <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
890 <expand macro="sanitize_query"/>
7
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
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parents: 6
diff changeset
891 </param>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
892 <expand macro="param_color_map"/>
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
893 <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
894 <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
895 <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
896 </param>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
897 <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"
iuc
parents: 0
diff changeset
898 <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"
iuc
parents: 0
diff changeset
899 <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
900 <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"
iuc
parents: 0
diff changeset
901 <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
902 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
903 <when value="pl.rank_genes_groups">
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
904 <expand macro="param_groups"/>
17
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iuc
parents: 16
diff changeset
905 <expand macro="param_n_genes" value="20"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
906 <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
907 <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
908 <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
909 <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
910 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
911 <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
912 <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
913 <conditional name="genes">
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
914 <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
915 <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
916 <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
917 </param>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
918 <when value="n_genes">
17
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iuc
parents: 16
diff changeset
919 <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
920 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
921 <when value="gene_names">
7
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iuc
parents: 6
diff changeset
922 <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
923 <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
924 </param>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
925 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
926 </conditional>
17
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iuc
parents: 16
diff changeset
927 <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
928 <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
929 <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
930 <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
931 <expand macro="conditional_stripplot"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
932 <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
933 <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
934 <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
935 <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
936 </param>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
937 </section>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
938 </when>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
939 <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
940 <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
941 <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
942 <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
943 <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
944 </when>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
945 <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
946 <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
947 <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
948 <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
949 <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
950 </when>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
951 <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
952 <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
953 <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
954 <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
955 <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
956 <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
957 </when>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
958 <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
959 <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
960 <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
961 <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
962 <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
963 <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
964 </when>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
965 <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
966 <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
967 <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
968 <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
969 <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
970 </when>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
971 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
972 <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
973 </inputs>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
974 <outputs>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
975 <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
976 <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
977 </data>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
978 <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
979 <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
980 <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
981 </collection>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
982 <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
983 <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
984 </data>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
985 <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
986 <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
987 <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
988 </collection>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
989 <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
990 <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
991 </data>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
992 <collection name="collection_svg" type="list" label="SVG plots from ${tool.name} (${method.method}) on ${on_string}">
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
993 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).svg" format="svg"/>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
994 <filter>format == 'svg' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
995 </collection>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
996 <data name="hidden_output" format="txt" label="Log file" hidden="true" >
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
997 <filter>advanced_common['show_log']</filter>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
998 </data>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
999 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix">
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1000 <filter>method['method'] == 'pl.paga'</filter>
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1001 </data>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1002 </outputs>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1003 <tests>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1004 <!-- 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
1005 <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
1006 <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
1007 <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
1008 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1009 <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
1010 <conditional name="type">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1011 <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
1012 <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
1013 <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
1014 </conditional>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1015 <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
1016 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1017 <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
1018 <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
1019 <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
1020 <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
1021 <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
1022 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1023 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1024 <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
1025 <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
1026 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1027 <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
1028 <assert_contents>
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="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
1030 <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
1031 <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
1032 <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
1033 <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
1034 <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
1035 <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
1036 <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
1037 <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
1038 <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
1039 <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
1040 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1041 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1042 <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
1043 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1044
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1045 <!-- 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
1046 <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
1047 <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
1048 <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
1049 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1050 <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
1051 <conditional name="type">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1052 <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
1053 <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
1054 <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
1055 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1056 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1057 <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
1058 <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
1059 <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
1060 <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
1061 <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
1062 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1063 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1064 <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
1065 <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
1066 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1067 <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
1068 <assert_contents>
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="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
1070 <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
1071 <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
1072 <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
1073 <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
1074 <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
1075 <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
1076 <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
1077 <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
1078 <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
1079 <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
1080 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1081 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1082 <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
1083 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1084
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1085 <!-- 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
1086 <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
1087 <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
1088 <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
1089 <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
1090 <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
1091 <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
1092 <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
1093 <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
1094 <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
1095 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1096 <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
1097 <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
1098 <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
1099 <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
1100 <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
1101 <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
1102 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1103 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1104 <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
1105 <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
1106 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1107 <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
1108 <assert_contents>
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="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
1110 <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
1111 <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
1112 <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
1113 <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
1114 <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
1115 <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
1116 <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
1117 <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
1118 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1119 </output>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1120 <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
1121 </test>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1122
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1123 <!-- test 4 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1124 <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
1125 <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
1126 <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
1127 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1128 <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
1129 <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
1130 <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
1131 <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
1132 <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
1133 <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
1134 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1135 <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
1136 <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
1137 <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
1138 <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
1139 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1140 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1141 <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
1142 <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
1143 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1144 <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
1145 <assert_contents>
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="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
1147 <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
1148 <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
1149 <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
1150 <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
1151 <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
1152 <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
1153 <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
1154 <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
1155 <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
1156 <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
1157 <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
1158 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1159 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1160 <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
1161 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1162
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1163 <!-- 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
1164 <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
1165 <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
1166 <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
1167 <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
1168 <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
1169 <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
1170 <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
1171 <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
1172 </conditional>
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="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
1174 <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
1175 <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
1176 <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
1177 <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
1178 <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
1179 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1180 <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
1181 <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
1182 <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
1183 <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
1184 <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
1185 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1186 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1187 <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
1188 <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
1189 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1190 <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
1191 <assert_contents>
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="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
1193 <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
1194 <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
1195 <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
1196 <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
1197 <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
1198 <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
1199 <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
1200 <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
1201 <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
1202 <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
1203 <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
1204 <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
1205 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1206 </output>
9
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927"
iuc
parents: 8
diff changeset
1207 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1208
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1209 <!-- 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
1210 <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
1211 <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
1212 <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
1213 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1214 <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
1215 <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
1216 <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
1217 <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
1218 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1219 <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
1220 <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
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="0"/>
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="1"/>
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="B cells"/>
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 <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
1227 <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
1228 <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
1229 <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
1230 </repeat>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1231 <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
1232 <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
1233 <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
1234 <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
1235 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1236 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1237 <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
1238 <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
1239 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1240 <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
1241 <assert_contents>
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="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
1243 <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
1244 <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
1245 <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
1246 <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
1247 <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
1248 <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
1249 <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
1250 <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
1251 <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
1252 <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
1253 <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
1254 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1255 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1256 <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
1257 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1258
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1259 <!-- 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
1260 <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
1261 <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
1262 <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
1263 <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
1264 <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
1265 <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
1266 <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
1267 <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
1268 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1269 <param name="gene_symbols" value="symbol"/>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1270 <param name="groupby" value="cell_type"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1271 <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
1272 <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
1273 <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
1274 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1275 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1276 <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
1277 <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
1278 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1279 <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
1280 <assert_contents>
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="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
1282 <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
1283 <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
1284 <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
1285 <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
1286 <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
1287 <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
1288 <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
1289 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1290 </output>
9
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927"
iuc
parents: 8
diff changeset
1291 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1292
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1293 <!-- 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
1294 <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
1295 <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
1296 <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
1297 <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
1298 <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
1299 <param name="gene_symbols" value="symbol"/>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1300 <param name="groupby" value="cell_type"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1301 <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
1302 <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
1303 <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
1304 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1305 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1306 <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
1307 <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
1308 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1309 <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
1310 <assert_contents>
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="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
1312 <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
1313 <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
1314 <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
1315 <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
1316 <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
1317 <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
1318 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1319 </output>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1320 </test>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1321
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1322 <!-- test 9 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1323 <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
1324 <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
1325 <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
1326 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1327 <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
1328 <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
1329 <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
1330 <param name="keys" value="n_genes, percent_mito, n_counts"/>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1331 </conditional>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1332 <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
1333 <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
1334 <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
1335 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1336 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1337 <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
1338 <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
1339 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1340 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1341 <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
1342 <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
1343 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1344 <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
1345 <assert_contents>
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="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
1347 <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
1348 <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
1349 <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
1350 <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
1351 <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
1352 <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
1353 <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
1354 <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
1355 <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
1356 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1357 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1358 <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
1359 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1360
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1361 <!-- 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
1362 <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
1363 <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
1364 <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
1365 <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
1366 <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
1367 <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
1368 <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
1369 <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
1370 <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
1371 <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
1372 </section>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1373 <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
1374 <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
1375 </section>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1376 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1377 <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
1378 <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
1379 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1380 <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
1381 <assert_contents>
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="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
1383 <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
1384 <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
1385 <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
1386 <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
1387 <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
1388 <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
1389 <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
1390 <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
1391 <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
1392 <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
1393 <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
1394 <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
1395 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1396 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1397 <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
1398 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1399
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1400 <!-- 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
1401 <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
1402 <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
1403 <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
1404 <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
1405 <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
1406 <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
1407 <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
1408 <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
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 <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
1411 <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
1412 <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
1413 <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
1414 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1415 <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
1416 <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
1417 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1418 <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
1419 <assert_contents>
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="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
1421 <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
1422 <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
1423 <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
1424 <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
1425 <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
1426 <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
1427 <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
1428 <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
1429 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1430 </output>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1431 <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
1432 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1433
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1434 <!-- 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
1435 <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
1436 <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
1437 <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
1438 <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
1439 <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
1440 <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
1441 <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
1442 <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
1443 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1444 <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
1445 <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
1446 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1447 <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
1448 <assert_contents>
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="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
1450 <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
1451 <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
1452 <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
1453 <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
1454 <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
1455 <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
1456 <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
1457 <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
1458 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1459 </output>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1460 <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
1461 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1462
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1463 <!-- test 13 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1464 <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
1465 <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
1466 <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
1467 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1468 <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
1469 <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
1470 <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
1471 <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
1472 </conditional>
17
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="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
1474 <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
1475 <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
1476 <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
1477 <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
1478 <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
1479 </conditional>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1480 <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
1481 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1482 <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
1483 <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
1484 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1485 <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
1486 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1487 <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
1488 <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
1489 <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
1490 <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
1491 <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
1492 <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
1493 <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
1494 <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
1495 <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
1496 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1497 </output>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1498 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1499
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1500 <!-- 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
1501 <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
1502 <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
1503 <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
1504 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1505 <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
1506 <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
1507 <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
1508 <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
1509 <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
1510 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1511 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1512 <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
1513 <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
1514 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1515 <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
1516 <assert_contents>
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="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
1518 <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
1519 <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
1520 <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
1521 <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
1522 <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
1523 <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
1524 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1525 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1526 <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
1527 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1528
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1529 <!-- 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
1530 <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
1531 <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
1532 <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
1533 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1534 <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
1535 <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
1536 <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
1537 <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
1538 <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
1539 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1540 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1541 <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
1542 <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
1543 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1544 <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
1545 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1546 <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
1547 <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
1548 <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
1549 <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
1550 <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
1551 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1552 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1553 <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
1554 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1555
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1556 <!-- 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
1557 <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
1558 <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
1559 <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
1560 <conditional name="method">
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1561 <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
1562 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1563 <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
1564 <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
1565 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1566 <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
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 <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
1569 <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
1570 <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
1571 <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
1572 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1573 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1574 <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
1575 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1576
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1577 <!-- 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
1578 <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
1579 <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
1580 <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
1581 <conditional name="method">
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1582 <param name="method" value="pl.scrublet_score_distribution"/>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1583 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1584 <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
1585 <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
1586 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1587 <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
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 <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
1590 <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
1591 <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
1592 <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
1593 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1594 </output>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1595 <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
1596 </test>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1597
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1598 <!-- test 18 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1599 <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
1600 <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
1601 <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
1602 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1603 <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
1604 <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
1605 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1606 <repeat name="components">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1607 <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
1608 <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
1609 </repeat>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1610 <repeat name="components">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1611 <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
1612 <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
1613 </repeat>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1614 <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
1615 <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
1616 <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
1617 <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
1618 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1619 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1620 <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
1621 <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
1622 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1623 <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
1624 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1625 <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
1626 <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
1627 <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
1628 <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
1629 <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
1630 <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
1631 <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
1632 <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
1633 <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
1634 <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
1635 <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
1636 <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
1637 <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
1638 <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
1639 <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
1640 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1641 </output>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1642 <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
1643 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1644
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1645 <!-- 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
1646 <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
1647 <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
1648 <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
1649 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1650 <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
1651 <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
1652 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1653 <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
1654 <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
1655 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1656 <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
1657 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1658 <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
1659 <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
1660 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1661 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1662 <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
1663 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1664
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1665 <!-- 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
1666 <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
1667 <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
1668 <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
1669 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1670 <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
1671 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1672 <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
1673 <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
1674 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1675 <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
1676 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1677 <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
1678 <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
1679 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1680 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1681 <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
1682 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1683
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1684 <!-- 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
1685 <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
1686 <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
1687 <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
1688 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1689 <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
1690 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1691 <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
1692 <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
1693 <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
1694 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1695 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1696 <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
1697 <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
1698 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1699 <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
1700 <assert_contents>
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="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
1702 <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
1703 <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
1704 <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
1705 <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
1706 <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
1707 <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
1708 <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
1709 <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
1710 <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
1711 <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
1712 <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
1713 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1714 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1715 <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
1716 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1717
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1718 <!-- 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
1719 <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
1720 <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
1721 <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
1722 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1723 <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
1724 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1725 <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
1726 <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
1727 <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
1728 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1729 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1730 <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
1731 <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
1732 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1733 <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
1734 <assert_contents>
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="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
1736 <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
1737 <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
1738 <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
1739 <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
1740 <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
1741 <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
1742 <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
1743 <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
1744 <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
1745 <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
1746 <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
1747 <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
1748 <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
1749 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1750 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1751 <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
1752 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1753
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1754 <!-- 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
1755 <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
1756 <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
1757 <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
1758 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1759 <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
1760 <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
1761 <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
1762 <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
1763 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1764 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1765 <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
1766 <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
1767 <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
1768 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1769 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1770 <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
1771 <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
1772 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1773 <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
1774 <assert_contents>
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="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
1776 <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
1777 <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
1778 <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
1779 <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
1780 <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
1781 <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
1782 <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
1783 <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
1784 <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
1785 <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
1786 <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
1787 <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
1788 <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
1789 <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
1790 <has_text_matching expression="hspace=0.25"/>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1791
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1792 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1793 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1794 <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
1795 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1796
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1797 <!-- 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
1798 <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
1799 <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
1800 <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
1801 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1802 <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
1803 <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
1804 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1805 <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
1806 <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
1807 <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
1808 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1809 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1810 <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
1811 <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
1812 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1813 <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
1814 <assert_contents>
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="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
1816 <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
1817 <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
1818 <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
1819 <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
1820 <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
1821 <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
1822 <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
1823 <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
1824 <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
1825 <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
1826 <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
1827 <has_text_matching expression="hspace=0.25"/>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1828
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1829 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1830 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1831 <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
1832 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1833
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1834 <!-- 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
1835 <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
1836 <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
1837 <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
1838 <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
1839 <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
1840 <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
1841 <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
1842 <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
1843 <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
1844 </conditional>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1845 <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
1846 <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
1847 <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
1848 </section>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1849 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1850 <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
1851 <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
1852 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1853 <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
1854 <assert_contents>
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="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
1856 <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
1857 <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
1858 <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
1859 <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
1860 <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
1861 <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
1862 <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
1863 <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
1864 <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
1865 <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
1866 <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
1867 <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
1868 <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
1869 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1870 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1871 <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
1872 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1873
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1874 <!-- 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
1875 <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
1876 <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
1877 <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
1878 <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
1879 <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
1880 <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
1881 </conditional>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1882 <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
1883 <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
1884 </section>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1885 <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
1886 <assert_contents>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1887 <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
1888 <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
1889 <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
1890 </assert_contents>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1891 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1892 <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
1893 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1894
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1895 <!-- 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
1896 <!-- test 27 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1897 <!-- <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
1898 <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
1899 <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
1900 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1901 <param name="method" value="pl.dpt_groups_pseudotime"/>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1902
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1903 </conditional>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1904 <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
1905 <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
1906 </section>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1907 <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
1908 <assert_contents>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1909 <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
1910 <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
1911 </assert_contents>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1912 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1913 <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
1914 </test> -->
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1915
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1916 <!-- 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
1917 <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
1918 <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
1919 <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
1920 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1921 <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
1922 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1923 <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
1924 <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
1925 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1926 <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
1927 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1928 <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
1929 <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
1930 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1931 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1932 <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
1933 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1934
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1935 <!-- test 29 -->
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1936 <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
1937 <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
1938 <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
1939 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1940 <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
1941 <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
1942 <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
1943 <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
1944 <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
1945 <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
1946 </conditional>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1947 <output name="out_png" file="pl.paga.paul15_gauss_braycurtis.png" ftype="png" compare="image_diff"/>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1948 <output name="anndata_out" ftype="h5ad">
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1949 <assert_contents>
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1950 <has_h5_keys keys="uns/paga"/>
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1951 </assert_contents>
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1952 </output>
11
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
1953 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1954
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1955 <!-- 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
1956 <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
1957 <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
1958 <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
1959 <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
1960 <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
1961 <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
1962 <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
1963 <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
1964 <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
1965 <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
1966 </conditional>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1967 <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
1968 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1969
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1970 <!-- test 31 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1971 <!-- <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
1972 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
1973 </test> -->
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1974
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1975 <!-- 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
1976 <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
1977 <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
1978 <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
1979 <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
1980 <param name="method" value="pl.rank_genes_groups"/>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1981 <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
1982 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1983 <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
1984 <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
1985 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1986 <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
1987 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1988 <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
1989 <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
1990 <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
1991 <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
1992 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
1993 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1994 <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
1995 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
1996
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
1997 <!-- 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
1998 <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
1999 <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
2000 <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
2001 <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
2002 <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
2003 <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
2004 <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
2005 <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
2006 </conditional>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2007 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2008 <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
2009 <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
2010 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2011 <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
2012 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2013 <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
2014 <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
2015 <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
2016 <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
2017 <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
2018 <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
2019 <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
2020 <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
2021 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2022 </output>
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2023 <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
2024 <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
2025 <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
2026 <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
2027 <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
2028 <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
2029 </output_collection>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2030 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
2031
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2032 <!-- 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
2033 <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
2034 <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
2035 <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
2036 <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
2037 <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
2038 <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
2039 <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
2040 <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
2041 <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
2042 <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
2043 <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
2044 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2045 <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
2046 </section>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2047 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2048 <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
2049 <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
2050 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2051 <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
2052 <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
2053 <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
2054 <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
2055 <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
2056 <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
2057 <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
2058 <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
2059 <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
2060 <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
2061 <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
2062 <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
2063 <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
2064 <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
2065 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2066 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2067 <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
2068 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
2069
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2070 <!-- 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
2071 <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
2072 <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
2073 <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
2074 <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
2075 <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
2076 <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
2077 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2078 <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
2079 <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
2080 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2081 <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
2082 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2083 <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
2084 <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
2085 <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
2086 <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
2087 <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
2088 <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
2089 <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
2090 <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
2091 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2092 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2093 <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
2094 </test>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2095
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2096 <!-- 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
2097 <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
2098 <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
2099 <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
2100 <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
2101 <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
2102 <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
2103 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2104 <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
2105 <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
2106 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2107 <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
2108 <assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2109 <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
2110 <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
2111 <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
2112 <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
2113 <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
2114 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2115 </output>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2116 <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
2117 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
2118
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2119 <!-- test 37 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2120 <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
2121 <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
2122 <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
2123 <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
2124 <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
2125 <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
2126 </conditional>
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2127 <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
2128 <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
2129 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2130 <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
2131 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2132 <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
2133 <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
2134 <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
2135 <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
2136 <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
2137 <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
2138 <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
2139 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2140 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2141 <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
2142 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
2143
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2144 <!-- 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
2145 <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
2146 <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
2147 <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
2148 <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
2149 <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
2150 <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
2151 <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
2152 <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
2153 </conditional>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2154 </conditional>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2155 <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
2156 <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
2157 </section>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2158 <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
2159 <assert_contents>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2160 <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
2161 <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
2162 <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
2163 <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
2164 </assert_contents>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2165 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2166 <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
2167 </test>
19
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 17
diff changeset
2168
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2169 <!-- 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
2170 <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
2171 <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
2172 <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
2173 <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
2174 <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
2175 <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
2176 <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
2177 <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
2178 </conditional>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2179 </conditional>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2180 <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
2181 <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
2182 </section>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2183 <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
2184 <assert_contents>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2185 <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
2186 <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
2187 <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
2188 <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
2189 </assert_contents>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 14
diff changeset
2190 </output>
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2191 <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
2192 </test>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2193
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2194 <!-- test 40 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2195 <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
2196 <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
2197 <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
2198 <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
2199 <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
2200 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2201 <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
2202 <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
2203 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2204 <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
2205 <assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2206 <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
2207 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2208 </output>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2209 <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
2210 </test>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2211 </tests>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2212 <help><![CDATA[
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2213 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
2214 =========================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2215
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2216 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
2217 (`.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
2218
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2219 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
2220 <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
2221
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2222 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
2223 ========================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2224
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2225 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
2226 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
2227 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
2228 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
2229 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
2230
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2231 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
2232 <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
2233
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2234 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
2235 =================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2236
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2237 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
2238 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
2239 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
2240 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
2241 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
2242 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
2243 equal to zero.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2244
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2245 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
2246 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
2247
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2248 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
2249 <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
2250
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2251 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
2252 ======================================
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2253
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2254 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
2255 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
2256
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2257 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
2258 <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
2259
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2260 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
2261 ==================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2262
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2263 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
2264
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2265 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
2266 <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
2267
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2268 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
2269 ===================================================
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2270
6
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
2271 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
2272 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
2273
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2274 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
2275 <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
2276
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2277 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
2278 ============================================================================
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 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
2281
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2282 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
2283 category.
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 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
2286 <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
2287
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2288 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
2289 ===========================================================
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 Wraps `seaborn.clustermap
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2292 <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
2293 `anndata.AnnData`.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2294
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2295 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
2296 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
2297
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2298 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
2299 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
2300
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2301 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
2302
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2303 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
2304 <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
2305
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2306 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
2307 =========================================================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2308
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2309 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
2310 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
2311 plotted as boxplots.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2312
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2313 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
2314
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2315 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
2316 <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
2317
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2318 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
2319 ===================================================================================
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2320
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2321 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
2322
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2323 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
2324 <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
2325
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2326 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
2327 =====================================================================================================================================
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2328
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2329 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
2330 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
2331
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2332 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
2333 <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
2334
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2335 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
2336 ===============================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2337
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2338 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
2339 <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
2340
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2341 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
2342 =====================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2343
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2344 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
2345 <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
2346
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2347 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
2348 ======================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2349
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2350 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
2351 <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
2352
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2353 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
2354 =========================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2355
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2356 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
2357 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
2358
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2359 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
2360 <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
2361
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2362 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
2363 =================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2364
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2365 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
2366 <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
2367
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2368 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
2369 ==================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2370
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2371 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
2372 <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
2373
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2374 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
2375 ==============================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2376
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2377 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
2378 <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
2379
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2380 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
2381 =================================================================
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2382
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2383 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
2384 <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
2385
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2386 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
2387 ==============================================================================================
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2388
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2389 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
2390 <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
2391
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2392 .. 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
2393 .. 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
2394 .. ===========================================================================================================
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2395
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2396 .. 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
2397 .. <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
2398
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2399 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
2400 =====================================================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2401
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2402 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
2403 <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
2404
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2405
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2406 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
2407 ====================================================================================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2408
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2409 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
2410
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2411 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
2412 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
2413 `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
2414
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2415 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
2416 <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
2417
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2418
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2419 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
2420 ==========================================================================================================
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2421
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2422 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
2423 <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
2424
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2425 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
2426 ======================================================================================================================
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2427
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2428 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
2429 <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
2430
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2431 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
2432 ===============================================================================
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2433
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2434 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
2435 <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
2436
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2437 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
2438 ==================================================================================
1
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2439
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
2440 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
2441 <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
2442
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2443 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
2444 ==================================================================================================
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2445
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2446 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
2447 <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
2448
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2449 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
2450 ====================================================================================
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2451
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2452 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
2453 <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
2454
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2455 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
2456 ====================================================================================
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 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
2459 <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
2460
3
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2461 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
2462 ==========================================================================================
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2463
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
2464 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
2465 <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
2466
17
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2467 ]]>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
2468 </help>
0
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2469 <expand macro="citations"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
2470 </tool>