Mercurial > repos > iuc > scanpy_filter

annotate filter.xml @ 22:5813f9920877 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 76bfefa9116713dc1078ae407ab6dd69ed14a244
author iuc
date Wed, 26 Mar 2025 09:43:50 +0000
parents 5b3c1679d29b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
21
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
1 <tool id="scanpy_filter" name="Scanpy filter" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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2 <description>mark and subsample</description>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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3 <macros>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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4 <import>macros.xml</import>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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5 </macros>
11
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
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6 <expand macro="bio_tools"/>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
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7 <expand macro="requirements">
713a0c65b1fe 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="0.2.3">scrublet</requirement>
713a0c65b1fe 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="0.1.4">scikit-misc</requirement>
713a0c65b1fe 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
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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11 <expand macro="version_command"/>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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12 <command detect_errors="exit_code"><![CDATA[
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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13 @CMD@
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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14 ]]></command>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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15 <configfiles>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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16 <configfile name="script_file"><![CDATA[
17
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iuc
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17 @CMD_IMPORTS@
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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18 @CMD_READ_INPUTS@
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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19
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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20 #if $method.method == 'pp.filter_cells'
1
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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21 sc.pp.filter_cells(
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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22 adata,
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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23 #if $method.filter.filter == 'min_counts'
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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24 min_counts=$method.filter.min_counts,
1
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
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25 #else if $method.filter.filter == 'max_counts'
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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26 max_counts=$method.filter.max_counts,
1
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
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27 #else if $method.filter.filter == 'min_genes'
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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28 min_genes=$method.filter.min_genes,
1
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
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29 #else if $method.filter.filter == 'max_genes'
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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30 max_genes=$method.filter.max_genes,
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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31 #end if
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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32 copy=False)
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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33
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
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34 @CMD_ANNDATA_WRITE_OUTPUTS@
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
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35
1
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
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36 #else if $method.method == 'pp.filter_genes'
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
37 sc.pp.filter_genes(
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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38 adata,
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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39 #if $method.filter.filter == 'min_counts'
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
40 min_counts=$method.filter.min_counts,
1
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
41 #else if $method.filter.filter == 'max_counts'
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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42 max_counts=$method.filter.max_counts,
1
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
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43 #else if $method.filter.filter == 'min_cells'
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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44 min_cells=$method.filter.min_cells,
1
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
45 #else if $method.filter.filter == 'max_cells'
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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46 max_cells=$method.filter.max_cells,
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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47 #end if
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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48 copy=False)
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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49
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
50 @CMD_ANNDATA_WRITE_OUTPUTS@
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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51
21
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
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52 #else if $method.method == 'filter_any'
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
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53 #if $method.filter.filter == 'key'
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
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54 #if $method.var_obs == 'var'
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
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55 filtered = adata.var['$method.filter.key']
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
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56 #else if $method.var_obs == 'obs'
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
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57 filtered = adata.obs['$method.filter.key']
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
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58 #end if
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
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59
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
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60 #if $method.filter.filter_key.type == 'number'
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
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61 #if $method.filter.filter_key.filter == 'equal'
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
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62 filtered = filtered == $method.filter.filter_key.value
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
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63 #else if $method.filter.filter_key.filter == 'equal'
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
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64 filtered = filtered != $method.filter.filter_key.value
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
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65 #else if $method.filter.filter_key.filter == 'less'
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
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66 filtered = filtered < $method.filter.filter_key.value
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
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67 #else if $method.filter.filter_key.filter == 'less_or_equal'
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
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68 filtered = filtered <= $method.filter.filter_key.value
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
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69 #else if $method.filter.filter_key.filter == 'greater'
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
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70 filtered = filtered > $method.filter.filter_key.value
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
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71 #else if $method.filter.filter_key.filter == 'greater_or_equal'
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
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72 filtered = filtered >= $method.filter.filter_key.value
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
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73 #end if
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
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74 #else if $method.filter.filter_key.type == 'text'
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
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75 #if $method.filter.filter_key.filter == 'equal'
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
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76 filtered = filtered == '$method.filter.filter_key.value'
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
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77 #else
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
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78 filtered = filtered != '$method.filter.filter_key.value'
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
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79 #end if
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
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80 #else if $method.filter.filter_key.type == 'boolean'
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
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81 filtered = filtered == $method.filter.filter_key.value
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
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82 #end if
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
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83
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
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84 #else if $method.filter.filter == 'index'
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
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85 #if str($method.filter.index.format) == 'file'
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
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86 with open('$method.filter.index.file', 'r') as filter_f:
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87 filters = [str(x.strip()) for x in filter_f.readlines()]
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88 filtered = filters
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89 #else
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90 #set $filters = [str(x.strip()) for x in $method.filter.index.text.split(',')]
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91 filtered = $filters
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92 #end if
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93 #end if
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94 print(filtered)
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95
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96 #if $method.var_obs == 'var'
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97 adata = adata[:,filtered]
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98 #else if $method.var_obs == 'obs'
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99 adata = adata[filtered, :]
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100 #end if
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101
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102 @CMD_ANNDATA_WRITE_OUTPUTS@
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103
1
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104 #else if $method.method == 'tl.filter_rank_genes_groups'
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105 sc.tl.filter_rank_genes_groups(
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106 adata,
12
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107 #if $method.key
1
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108 key='$method.key',
0
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109 #end if
12
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110 #if $method.groupby
1
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111 groupby='$method.groupby',
0
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112 #end if
1
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113 use_raw=$method.use_raw,
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114 key_added='$method.key_added',
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115 min_in_group_fraction=$method.min_in_group_fraction,
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116 max_out_group_fraction=$method.max_out_group_fraction,
17
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117 min_fold_change=$method.min_fold_change,
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118 compare_abs=$method.compare_abs)
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119
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120 # Temporary fix for Issue reported here: https://github.com/scverse/anndata/issues/726
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121 # Check and convert elements in 'rank_genes_groups_filtered' to strings
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122 if 'rank_genes_groups_filtered' in adata.uns:
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123 for key, value in adata.uns['rank_genes_groups_filtered'].items():
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124 if not isinstance(value, str):
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125 adata.uns['rank_genes_groups_filtered'][key] = str(value)
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126
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127 @CMD_ANNDATA_WRITE_OUTPUTS@
0
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128
1
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129 #else if $method.method == "pp.highly_variable_genes"
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130 sc.pp.highly_variable_genes(
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131 adata=adata,
0
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132 flavor='$method.flavor.flavor',
17
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133 #if $method.flavor.flavor == 'seurat':
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134 min_mean=$method.flavor.min_mean,
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135 max_mean=$method.flavor.max_mean,
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136 min_disp=$method.flavor.min_disp,
1
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137 #if str($method.flavor.max_disp) != ''
17
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138 max_disp=$method.flavor.max_disp,
0
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139 #end if
17
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140 #else if $method.flavor.flavor == 'cell_ranger':
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141 n_top_genes=$method.flavor.n_top_genes,
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142 #else if $method.flavor.flavor == 'seurat_v3':
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143 n_top_genes=$method.flavor.n_top_genes,
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144 span=$method.flavor.span,
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145 #else if $method.flavor.flavor == 'seurat_v3_paper':
0
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146 n_top_genes=$method.flavor.n_top_genes,
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147 #end if
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148 n_bins=$method.n_bins,
1
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149 subset=$method.subset,
17
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150 #if $method.layer != ''
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151 layer='$method.layer',
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152 #end if
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153 #if $method.batch_key != ''
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154 layer='$method.batch_key',
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155 #end if
1
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156 inplace=True)
0
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157
17
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158 @CMD_ANNDATA_WRITE_OUTPUTS@
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159
1
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160 #else if $method.method == 'pp.subsample'
0
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161 sc.pp.subsample(
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162 data=adata,
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163 #if $method.type.type == 'fraction'
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164 fraction=$method.type.fraction,
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165 #else if $method.type.type == 'n_obs'
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166 n_obs=$method.type.n_obs,
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167 #end if
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168 random_state=$method.random_state,
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169 copy=False)
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170
17
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171 @CMD_ANNDATA_WRITE_OUTPUTS@
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172
1
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173 #else if $method.method == "pp.downsample_counts"
17
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174 #if str($method.counts_per_cell) != ''
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175 print("Sum of counts for the first cell before:", adata.X[0, :].sum())
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176 print("Sum of counts for the last cell before:", adata.X[adata.X.shape[0]-1, :].sum())
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177 #else if str($method.total_counts) != ''
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178 print("Sum of total counts before:", adata.X.sum())
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179 #end if
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180
1
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181 sc.pp.downsample_counts(
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182 adata=adata,
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183 #if str($method.counts_per_cell) != ''
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184 counts_per_cell=$method.counts_per_cell,
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185 #end if
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186 #if str($method.total_counts) != ''
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187 total_counts=$method.total_counts,
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188 #end if
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189 random_state=$method.random_state,
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190 replace=$method.replace,
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191 copy=False)
15
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192
17
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193 #if str($method.counts_per_cell) != ''
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194 print("Sum of counts for the first cell after:", adata.X[0, :].sum())
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195 print("Sum of counts for the last cell after:", adata.X[adata.X.shape[0]-1, :].sum())
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196 #else if str($method.total_counts) != ''
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197 print("Sum of total counts after:", adata.X.sum())
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198 #end if
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199
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200 @CMD_ANNDATA_WRITE_OUTPUTS@
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201
15
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202 #else if $method.method == "filter_marker"
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203
17
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204 #if $method.layer_selection.use_raw == 'False':
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205 adata.X = adata.layers['$method.layer_selection.layer']
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206 #end if
15
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207
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208 def check_marker(adata, group, gene, thresh_mean, thresh_frac, groupby):
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209 filtered_data = adata[adata.obs[groupby] == group, adata.var_names == gene]
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210 mean_expression = np.mean(filtered_data.X)
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211 frac_cell_mean_expression = len(filtered_data.X[filtered_data.X > mean_expression]) / filtered_data.n_obs
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212 if ( mean_expression > thresh_mean and frac_cell_mean_expression >= thresh_frac ):
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213 return(True)
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214 return(False)
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215
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216 header='infer'
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217
17
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218 #if $method.header == 'not_included':
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219 header=None
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220 #end if
15
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221
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222 marker_list={key: list(value.values()) for key, value in pd.read_csv('$method.markerfile', sep='\t', index_col=0, header=header).to_dict(orient='index').items()}
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223
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224 for key, value in marker_list.items():
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225 marker_list[key] = [x for x in value if check_marker(adata, key, x, $method.thresh_mean, $method.thresh_frac, '$method.groupby')]
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226
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227 # Find the maximum length of lists
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228 max_len = max(len(lst) for lst in marker_list.values())
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229
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230 # Fill smaller lists with empty values
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231 for key, value in marker_list.items():
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232 marker_list[key] = value + [''] * (max_len - len(value))
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233
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234 df = pd.DataFrame(marker_list).T
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235 df.to_csv('marker.tsv', sep='\t', index=True)
0
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236
17
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237 #else if $method.method == "pp.scrublet"
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238 sc.pp.scrublet(
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239 adata,
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240 #if $method.batch_key != ''
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241 batch_key='$method.batch_key',
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242 #end if
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243 sim_doublet_ratio=$method.sim_doublet_ratio,
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244 expected_doublet_rate=$method.expected_doublet_rate,
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245 stdev_doublet_rate=$method.stdev_doublet_rate,
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246 synthetic_doublet_umi_subsampling=$method.synthetic_doublet_umi_subsampling,
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247 knn_dist_metric='$method.knn_dist_metric',
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248 normalize_variance=$method.normalize_variance,
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249 log_transform=$method.log_transform,
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250 mean_center=$method.mean_center,
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251 n_prin_comps=$method.n_prin_comps,
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252 use_approx_neighbors=$method.use_approx_neighbors,
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253 get_doublet_neighbor_parents=$method.get_doublet_neighbor_parents,
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254 #if str($method.n_neighbors) != ''
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255 n_neighbors=$method.n_neighbors,
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256 #end if
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257 #if str($method.threshold) != ''
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258 threshold=$method.threshold,
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259 #end if
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260 random_state=$method.random_state)
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261
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262 @CMD_ANNDATA_WRITE_OUTPUTS@
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263 #end if
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264 ]]>
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265 </configfile>
0
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266 </configfiles>
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267 <inputs>
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268 <expand macro="inputs_anndata"/>
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269 <conditional name="method">
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270 <param argument="method" type="select" label="Method used for filtering">
3
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271 <option value="pp.filter_cells">Filter cell outliers based on counts and numbers of genes expressed, using 'pp.filter_cells'</option>
0a6de5e65992 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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272 <option value="pp.filter_genes">Filter genes based on number of cells or counts, using 'pp.filter_genes'</option>
21
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273 <option value="filter_any">Filter on any column of observations or variables</option>
3
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274 <option value="tl.filter_rank_genes_groups">Filters out genes based on fold change and fraction of genes expressing the gene within and outside the groupby categories, using 'tl.filter_rank_genes_groups'</option>
0a6de5e65992 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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275 <option value="pp.highly_variable_genes">Annotate (and filter) highly variable genes, using 'pp.highly_variable_genes'</option>
0a6de5e65992 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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276 <option value="pp.subsample">Subsample to a fraction of the number of observations, using 'pp.subsample'</option>
0a6de5e65992 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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277 <option value="pp.downsample_counts">Downsample counts from count matrix, using 'pp.downsample_counts'</option>
15
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278 <option value="filter_marker">Filter markers from count matrix and marker list</option>
17
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279 <option value="pp.scrublet">Predict doublets using 'pp.scrublet'</option>
0
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280 </param>
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281 <when value="pp.filter_cells">
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282 <conditional name="filter">
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283 <param argument="filter" type="select" label="Filter">
17
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284 <option value="min_counts" selected="true">Minimum number of counts</option>
0
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285 <option value="max_counts">Maximum number of counts</option>
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286 <option value="min_genes">Minimum number of genes expressed</option>
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287 <option value="max_genes">Maximum number of genes expressed</option>
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288 </param>
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289 <when value="min_counts">
21
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290 <param argument="min_counts" type="integer" min="0" value="0" label="Minimum number of counts required for a cell to pass filtering"/>
0
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291 </when>
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292 <when value="max_counts">
21
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293 <param argument="max_counts" type="integer" min="0" value="100000000" label="Maximum number of counts required for a cell to pass filtering"/>
0
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294 </when>
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295 <when value="min_genes">
21
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296 <param argument="min_genes" type="integer" min="0" value="0" label="Minimum number of genes expressed required for a cell to pass filtering"/>
17
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297 </when>
0
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298 <when value="max_genes">
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299 <param argument="max_genes" type="integer" min="0" value="100000000" label="Maximum number of genes expressed required for a cell to pass filtering"/>
0
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300 </when>
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301 </conditional>
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302 </when>
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303 <when value="pp.filter_genes">
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304 <conditional name="filter">
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305 <param argument="filter" type="select" label="Filter">
17
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306 <option value="min_counts" selected="true">Minimum number of counts</option>
0
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307 <option value="max_counts">Maximum number of counts</option>
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308 <option value="min_cells">Minimum number of cells expressed</option>
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309 <option value="max_cells">Maximum number of cells expressed</option>
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310 </param>
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311 <when value="min_counts">
21
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312 <param argument="min_counts" type="integer" min="0" value="" optional="true" label="Minimum number of counts required for a gene to pass filtering"/>
0
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313 </when>
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314 <when value="max_counts">
21
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315 <param argument="max_counts" type="integer" min="0" value="" optional="true" label="Maximum number of counts required for a gene to pass filtering"/>
0
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316 </when>
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317 <when value="min_cells">
21
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318 <param argument="min_cells" type="integer" min="0" value="" optional="true" label="Minimum number of cells expressed required for a gene to pass filtering"/>
17
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319 </when>
0
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320 <when value="max_cells">
21
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321 <param argument="max_cells" type="integer" min="0" value="" optional="true" label="Maximum number of cells expressed required for a gene to pass filtering"/>
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322 </when>
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323 </conditional>
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324 </when>
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325 <when value="filter_any">
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326 <param name="var_obs" type="select" label="What to filter?">
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327 <option value="var">Variables (var)</option>
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328 <option value="obs">Observations (obs)</option>
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329 </param>
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330 <conditional name="filter">
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331 <param name="filter" type="select" label="Type of filtering?">
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332 <option value="key">By key (column) values</option>
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333 <option value="index">By index (row)</option>
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334 </param>
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335 <when value="key">
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336 <param name="key" type="text" value="n_genes" label="Key to filter"/>
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337 <conditional name="filter_key">
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338 <param name="type" type="select" label="Type of value to filter">
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339 <option value="number">Number</option>
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340 <option value="text">Text</option>
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341 <option value="boolean">Boolean</option>
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342 </param>
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343 <when value="number">
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344 <param name="filter" type="select" label="Filter">
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345 <option value="equal">equal to</option>
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346 <option value="not_equal">not equal to</option>
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347 <option value="less">less than</option>
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348 <option value="less_or_equal">less than or equal to</option>
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349 <option value="greater">greater than</option>
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parents: 17
diff changeset
350 <option value="greater_or_equal">greater than or equal to</option>
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parents: 17
diff changeset
351 </param>
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parents: 17
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352 <param name="value" type="float" value="2500" label="Value"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
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parents: 17
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353 </when>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
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parents: 17
diff changeset
354 <when value="text">
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parents: 17
diff changeset
355 <param name="filter" type="select" label="Filter">
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
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parents: 17
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356 <option value="equal">equal to</option>
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parents: 17
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357 <option value="not_equal">not equal to</option></param>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
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parents: 17
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358 <param name="value" type="text" value="2500" label="Value"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
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parents: 17
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359 </when>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
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parents: 17
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360 <when value="boolean">
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
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parents: 17
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361 <param name="value" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Value to keep"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
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parents: 17
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362 </when>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
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parents: 17
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363 </conditional>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
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parents: 17
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364 </when>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
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parents: 17
diff changeset
365 <when value="index">
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parents: 17
diff changeset
366 <conditional name="index">
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
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parents: 17
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367 <param name="format" type="select" label="Format for the filter by index">
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
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parents: 17
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368 <option value="file">File</option>
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parents: 17
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369 <option value="text" selected="true">Text</option>
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parents: 17
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370 </param>
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parents: 17
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371 <when value="text">
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parents: 17
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372 <param name="text" type="text" value="" label="List of index to keep" help="Indexes separated by a comma"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
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parents: 17
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373 </when>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
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parents: 17
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374 <when value="file">
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parents: 17
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375 <param name="file" type="data" format="txt" label="File with the list of index to keep" help="One index per line"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
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parents: 17
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376 </when>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
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parents: 17
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377 </conditional>
0
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diff changeset
378 </when>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
379 </conditional>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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380 </when>
1
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parents: 0
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381 <when value="tl.filter_rank_genes_groups">
7
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parents: 6
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382 <param argument="key" type="text" optional="true" label="Key in adata.uns where the rank_genes_groups output is stored">
17
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parents: 16
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383 <expand macro="sanitize_query"/>
7
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parents: 6
diff changeset
384 </param>
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parents: 6
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385 <param argument="groupby" type="text" optional="true" label="The key of the observations grouping to consider">
17
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parents: 16
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386 <expand macro="sanitize_query"/>
7
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parents: 6
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387 </param>
1
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parents: 0
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388 <expand macro="param_use_raw"/>
7
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parents: 6
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389 <param argument="key_added" type="text" value="rank_genes_groups_filtered" label="Key that will contain new values">
17
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parents: 16
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390 <expand macro="sanitize_query"/>
7
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parents: 6
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391 </param>
1
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parents: 0
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392 <param argument="min_in_group_fraction" type="float" min="0" max="1" value="0.25" label="Minimum fraction of genes expressing the gene within the categories"/>
6a76b60e05f5 "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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393 <param argument="max_out_group_fraction" type="float" min="0" max="1" value="0.5" label="Maximum fraction of genes expressing the gene outside the categories"/>
17
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394 <param argument="min_fold_change" type="integer" value="1" label="Minimum fold change"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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395 <param argument="compare_abs" type="boolean" truevalue="True" falsevalue="False" checked="false" label="If selected, compare absolute values of log fold change with min_fold_change"/>
1
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parents: 0
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396 </when>
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parents: 0
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397 <when value="pp.highly_variable_genes">
0
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398 <conditional name='flavor'>
17
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399 <param argument="flavor" type="select" label="Choose the flavor for identifying highly variable genes" help="Expects logarithmized data, except when flavor='seurat_v3'/'seurat_v3_paper', in which count">
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400 <option value="seurat" selected="true">Seurat</option>
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parents: 2
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401 <option value="cell_ranger">Cell Ranger</option>
17
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parents: 16
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402 <option value="seurat_v3">Seurat v3</option>
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parents: 16
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403 <option value="seurat_v3_paper">Seurat v3 (paper)</option>
0
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404 </param>
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405 <when value="seurat">
1
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parents: 0
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406 <param argument="min_mean" type="float" value="0.0125" label="Minimal mean cutoff"/>
6a76b60e05f5 "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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407 <param argument="max_mean" type="float" value="3" label="Maximal mean cutoff"/>
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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408 <param argument="min_disp" type="float" value="0.5" label="Minimal normalized dispersion cutoff"/>
6a76b60e05f5 "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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409 <param argument="max_disp" type="float" value="" optional="true" label="Maximal normalized dispersion cutoff"/>
0
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410 </when>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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411 <when value="cell_ranger">
1
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parents: 0
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412 <param argument="n_top_genes" type="integer" value="" label="Number of highly-variable genes to keep"/>
0
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413 </when>
17
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parents: 16
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414 <when value="seurat_v3">
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parents: 16
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415 <param argument="n_top_genes" type="integer" value="" optional="false" label="Number of highly-variable genes to keep"/>
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416 <param argument="span" type="float" value="0.3" label="The fraction of the data (cells) used when estimating the variance in the loess model fit"/>
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parents: 16
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417 </when>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 16
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418 <when value="seurat_v3_paper">
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419 <param argument="n_top_genes" type="integer" value="" optional="false" label="Number of highly-variable genes to keep"/>
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parents: 16
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420 </when>
0
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421 </conditional>
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422 <param argument="n_bins" type="integer" value="20" label="Number of bins for binning the mean gene expression" help="Normalization is done with respect to each bin. If just a single gene falls into a bin, the normalized dispersion is artificially set to 1"/>
3
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423 <param argument="subset" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Inplace subset to highly-variable genes?" help="Otherwise it merely indicates highly variable genes."/>
17
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parents: 16
diff changeset
424 <expand macro="param_layer"/>
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parents: 16
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425 <param argument="batch_key" type="text" value="" label="Specify the batch key" help="If specified, highly-variable genes are selected within each batch separately and merged.">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 16
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426 <expand macro="sanitize_query"/>
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parents: 16
diff changeset
427 </param>
0
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428 </when>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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429 <when value="pp.subsample">
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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430 <conditional name="type">
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431 <param name="type" type="select" label="Type of subsampling">
17
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432 <option value="fraction" selected="true">By fraction</option>
0
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433 <option value="n_obs">By number of observation</option>
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434 </param>
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435 <when value="fraction">
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436 <param argument="fraction" type="float" min="0" value="" label="Subsample to this 'fraction' of the number of observations"/>
0
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437 </when>
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438 <when value="n_obs">
1
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parents: 0
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439 <param argument="n_obs" type="integer" min="0" value="" label="Subsample to this number of observations"/>
0
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440 </when>
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441 </conditional>
1
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442 <param argument="random_state" type="integer" value="0" label="Random seed to change subsampling"/>
6a76b60e05f5 "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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443 </when>
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444 <when value="pp.downsample_counts">
6a76b60e05f5 "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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445 <param argument="counts_per_cell" type="integer" min="0" optional="true" label="Target total counts per cell" help="If a cell has more than ‘counts_per_cell’, it will be downsampled to this number. Resulting counts can be specified on a per cell basis by passing an array."/>
6a76b60e05f5 "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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446 <param argument="total_counts" type="integer" min="0" optional="true" label="Target total counts" help="If the count matrix has more than total_counts it will be downsampled to have this number."/>
6a76b60e05f5 "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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447 <param argument="random_state" type="integer" value="0" label="Random seed to change subsampling"/>
6a76b60e05f5 "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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448 <param argument="replace" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Sample the counts with replacement?"/>
0
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449 </when>
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450 <when value="filter_marker">
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451 <param argument="markerfile" type="data" format="tabular" label="List of markers" help="This should be a tsv where row = group (e.g. celltypes) and columns = markers."></param>
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452 <param name="header" type="boolean" truevalue="included" falsevalue="not_included" checked="true" label="Header is included in the list of markers?"/>
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453 <param argument="thresh_mean" type="float" min="0.0" value="1.0" label="Minimal average count of all cells of a group (e.g., celltype) for a particular marker" help="Increasing the threshold will result in a smaller marker set."/>
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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454 <param argument="thresh_frac" type="float" min="0.0" max="1.0" value="0.1" label="Minimal fractions of cells that has a higher count than the average count of all cells of the group for the marker" help="Increasing this threshold might remove marker outliers."/>
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455 <conditional name="layer_selection">
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456 <param name="use_raw" type="select" label="Use .X of adata to perform the filtering">
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457 <option value="True" selected="true">Yes</option>
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458 <option value="False">No</option>
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459 </param>
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460 <when value="False">
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461 <param argument="layer" type="text" value="" label="Key from adata.layers whose value will be used to filter" help="If layers specified then use adata.layers[layer]."/>
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462 </when>
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463 <when value="True"/>
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464 </conditional>
17
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465 <param argument="groupby" type="text" value="" label="The key of the observation grouping to consider (e.g., celltype)">
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466 <expand macro="sanitize_query"/>
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diff changeset
467 </param>
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diff changeset
468 </when>
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469 <when value="pp.scrublet">
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470 <param argument="batch_key" type="text" value="" optional="true" label="Batch key for the concatenate">
15
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471 <expand macro="sanitize_query" />
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472 </param>
17
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473 <param argument="sim_doublet_ratio" type="float" value="2.0" label="Number of doublets to simulate relative to the number of observed transcriptomes"/>
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474 <param argument="expected_doublet_rate" type="float" value="0.05" label="The estimated doublet rate for the experiment"/>
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475 <param argument="stdev_doublet_rate" type="float" value="0.02" label="Uncertainty in the expected doublet rate"/>
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476 <param argument="synthetic_doublet_umi_subsampling" type="float" value="1.0" label="Rate for sampling UMIs when creating synthetic doublets" help="f 1.0, each doublet is created by simply adding the UMI counts from two randomly sampled observed transcriptomes. For values less than 1, the UMI counts are added and then randomly sampled at the specified rate."/>
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diff changeset
477 <param name="knn_dist_metric" type="select" label="Distance metric used when finding nearest neighbors">
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478 <expand macro="distance_metric_options"/>
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479 </param>
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480 <param argument="normalize_variance" type="boolean" truevalue="True" falsevalue="False" checked="true" label="normalize the data such that each gene has a variance of 1"/>
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481 <param argument="log_transform" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Whether to use log1p() to log-transform the data prior to PCA"/>
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482 <param argument="mean_center" type="boolean" truevalue="True" falsevalue="False" checked="true" label="If True, center the data such that each gene has a mean of 0"/>
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483 <param argument="n_prin_comps" type="integer" value="30" label="Number of principal components used to embed the transcriptomes prior to k-nearest-neighbor graph construction"/>
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484 <param argument="use_approx_neighbors" type="boolean" truevalue="True" falsevalue="None" checked="false" label="Use approximate nearest neighbor method (annoy) for the KNN classifier"/>
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485 <param argument="get_doublet_neighbor_parents" type="boolean" truevalue="True" falsevalue="False" checked="false" label="If True, return (in .uns) the parent transcriptomes that generated the doublet neighbors of each observed transcriptome" help="This information can be used to infer the cell states that generated a given doublet state."/>
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486 <param argument="n_neighbors" type="integer" value="" optional="true" label="Number of neighbors used to construct the KNN graph of observed transcriptomes and simulated doublets"/>
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487 <param argument="threshold" type="float" value="" optional="true" label="Doublet score threshold for calling a transcriptome a doublet" help="If None, this is set automatically"/>
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488 <param name="random_state" type="integer" value="0" label="Initial state for doublet simulation and nearest neighbors"/>
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489 </when>
0
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490 </conditional>
6
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491 <expand macro="inputs_common_advanced"/>
0
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492 </inputs>
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493 <outputs>
17
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494 <expand macro="anndata_outputs">
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495 <filter>method['method'] != 'filter_marker'</filter>
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496 </expand>
15
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497 <data name="marker_out" format="tabular" from_work_dir="marker.tsv" label="${tool.name} on ${on_string}: Markers">
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498 <filter>method['method'] == 'filter_marker'</filter>
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499 </data>
0
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500 </outputs>
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501 <tests>
17
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502 <!-- test 1 -->
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503 <test expect_num_outputs="2">
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504 <param name="adata" value="krumsiek11.h5ad"/>
0
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505 <conditional name="method">
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506 <param name="method" value="pp.filter_cells"/>
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507 <conditional name="filter">
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508 <param name="filter" value="min_counts"/>
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509 <param name="min_counts" value="3"/>
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510 </conditional>
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511 </conditional>
17
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512 <section name="advanced_common">
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diff changeset
513 <param name="show_log" value="true"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
514 </section>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
515 <assert_stdout>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
516 <has_text_matching expression="336 × 11"/>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
517 </assert_stdout>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
518 <output name="hidden_output">
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
519 <assert_contents>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
520 <has_text_matching expression="sc.pp.filter_cells"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
521 <has_text_matching expression="min_counts=3"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
522 </assert_contents>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
523 </output>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
524 <output name="anndata_out" ftype="h5ad">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
525 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
526 <has_h5_keys keys="obs/cell_type"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
527 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
528 </output>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
529 </test>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
530
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
531 <!-- test 2 -->
11
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
532 <test expect_num_outputs="2">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
533 <param name="adata" value="krumsiek11.h5ad"/>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
534 <conditional name="method">
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
535 <param name="method" value="pp.filter_cells"/>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
536 <conditional name="filter">
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
537 <param name="filter" value="max_genes"/>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
538 <param name="max_genes" value="10"/>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
539 </conditional>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
540 </conditional>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
541 <section name="advanced_common">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
542 <param name="show_log" value="true"/>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
543 </section>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
544 <assert_stdout>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
545 <has_text_matching expression="354 × 11"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
546 </assert_stdout>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
547 <output name="hidden_output">
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
548 <assert_contents>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
549 <has_text_matching expression="sc.pp.filter_cells"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
550 <has_text_matching expression="adata"/>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
551 <has_text_matching expression="max_genes=10"/>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
552 </assert_contents>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
553 </output>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
554 <output name="anndata_out" ftype="h5ad">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
555 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
556 <has_h5_keys keys="obs/cell_type"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
557 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
558 </output>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
559 </test>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
560
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
561 <!-- test 3 -->
11
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
562 <test expect_num_outputs="2">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
563 <param name="adata" value="krumsiek11.h5ad"/>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
564 <conditional name="method">
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
565 <param name="method" value="pp.filter_genes"/>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
566 <conditional name="filter">
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
567 <param name="filter" value="min_counts"/>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
568 <param name="min_counts" value="100"/>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
569 </conditional>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
570 </conditional>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
571 <section name="advanced_common">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
572 <param name="show_log" value="true"/>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
573 </section>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
574 <assert_stdout>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
575 <has_text_matching expression="640 × 8"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
576 </assert_stdout>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
577 <output name="hidden_output">
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
578 <assert_contents>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
579 <has_text_matching expression="sc.pp.filter_genes"/>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
580 <has_text_matching expression="min_counts=100"/>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
581 </assert_contents>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
582 </output>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
583 <output name="anndata_out" ftype="h5ad">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
584 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
585 <has_h5_keys keys="obs/cell_type"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
586 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
587 </output>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
588 </test>
11
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
589
21
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
590 <test expect_num_outputs="1">
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
591 <!-- test 4 -->
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
592 <param name="adata" value="krumsiek11.h5ad"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
593 <conditional name="method">
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
594 <param name="method" value="filter_any"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
595 <param name="var_obs" value="var"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
596 <conditional name="filter">
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
597 <param name="filter" value="index"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
598 <conditional name="index">
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
599 <param name="format" value="text"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
600 <param name="text" value="Gata2,EKLF"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
601 </conditional>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
602 </conditional>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
603 </conditional>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
604 <assert_stdout>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
605 <has_text_matching expression="640 × 2"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
606 </assert_stdout>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
607 <output name="anndata_out" ftype="h5ad">
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
608 <assert_contents>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
609 <has_h5_keys keys="obs/cell_type"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
610 <has_h5_keys keys="uns/highlights"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
611 <has_h5_keys keys="uns/iroot"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
612 </assert_contents>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
613 </output>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
614 </test>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
615 <test expect_num_outputs="1">
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
616 <!-- test 5 -->
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
617 <param name="adata" value="krumsiek11.h5ad"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
618 <conditional name="method">
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
619 <param name="method" value="filter_any"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
620 <param name="var_obs" value="obs"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
621 <conditional name="filter">
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
622 <param name="filter" value="key"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
623 <param name="key" value="cell_type"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
624 <conditional name="filter_key">
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
625 <param name="type" value="text"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
626 <param name="filter" value="equal"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
627 <param name="value" value="progenitor"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
628 </conditional>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
629 </conditional>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
630 </conditional>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
631 <assert_stdout>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
632 <has_text_matching expression="320 × 11"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
633 </assert_stdout>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
634 <output name="anndata_out" ftype="h5ad">
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
635 <assert_contents>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
636 <has_h5_keys keys="obs/cell_type"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
637 <has_h5_keys keys="uns/highlights"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
638 <has_h5_keys keys="uns/iroot"/>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
639 </assert_contents>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
640 </output>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
641 </test>
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
642
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
643 <!-- test 6 -->
11
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
644 <!-- Fails to write to anndata after tl.filter_rank_genes_groups
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
645 Issue has been reported here: https://github.com/scverse/anndata/issues/726
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
646 The current fix is: del adata.uns['rank_genes_groups_filtered'] -->
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
647 <!-- The issue is fixed in the script here -->
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
648 <test expect_num_outputs="2">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
649 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
11
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
650 <conditional name="method">
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
651 <param name="method" value="tl.filter_rank_genes_groups"/>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
652 <param name="key" value="rank_genes_groups"/>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
653 <param name="min_fold_change" value="3"/>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
654 </conditional>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
655 <section name="advanced_common">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
656 <param name="show_log" value="true"/>
11
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
657 </section>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
658 <output name="hidden_output">
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
659 <assert_contents>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
660 <has_text_matching expression="tl.filter_rank_genes_groups"/>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
661 <has_text_matching expression="key='rank_genes_groups'"/>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
662 <has_text_matching expression="use_raw=False"/>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
663 <has_text_matching expression="key_added='rank_genes_groups_filtered'"/>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
664 <has_text_matching expression="min_in_group_fraction=0.25"/>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
665 <has_text_matching expression="max_out_group_fraction=0.5"/>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
666 <has_text_matching expression="min_fold_change=3"/>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
667 </assert_contents>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
668 </output>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
669 <output name="anndata_out" ftype="h5ad">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
670 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
671 <has_h5_keys keys="uns/rank_genes_groups_filtered"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
672 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
673 </output>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
674 </test>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
675
21
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iuc
parents: 17
diff changeset
676 <!-- test 7 -->
11
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
677 <test expect_num_outputs="2">
1
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
678 <param name="adata" value="blobs.h5ad"/>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
679 <conditional name="method">
1
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
680 <param name="method" value="pp.highly_variable_genes"/>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
681 </conditional>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
682 <section name="advanced_common">
17
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iuc
parents: 16
diff changeset
683 <param name="show_log" value="true"/>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
684 </section>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
685 <output name="hidden_output">
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
686 <assert_contents>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
687 <has_text_matching expression="sc.pp.highly_variable_genes"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
688 <has_text_matching expression="flavor='seurat'"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
689 <has_text_matching expression="min_mean=0.0125"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
690 <has_text_matching expression="max_mean=3"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
691 <has_text_matching expression="min_disp=0.5"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
692 <has_text_matching expression="n_bins=20"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
693 <has_text_matching expression="subset=False"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
694 </assert_contents>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
695 </output>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
696 <output name="anndata_out" ftype="h5ad">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
697 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
698 <has_h5_keys keys="var/highly_variable,var/means,var/dispersions,var/dispersions_norm"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
699 <has_h5_keys keys="uns/hvg"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
700 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
701 </output>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
702 </test>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
703
21
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
704 <!-- test 8 -->
11
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
705 <test expect_num_outputs="2">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
706 <param name="adata" value="krumsiek11.h5ad"/>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
707 <conditional name="method">
1
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
708 <param name="method" value="pp.highly_variable_genes"/>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
709 <conditional name="flavor">
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
710 <param name="flavor" value="cell_ranger"/>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
711 <param name="n_top_genes" value="2"/>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
712 </conditional>
3
0a6de5e65992 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
713 <param name="subset" value="true"/>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
714 </conditional>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
715 <section name="advanced_common">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
716 <param name="show_log" value="true"/>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
717 </section>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
718 <output name="hidden_output">
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
719 <assert_contents>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
720 <has_text_matching expression="sc.pp.highly_variable_genes"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
721 <has_text_matching expression="flavor='cell_ranger'"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
722 <has_text_matching expression="n_top_genes=2"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
723 <has_text_matching expression="n_bins=20"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
724 <has_text_matching expression="subset=True"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
725 </assert_contents>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
726 </output>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
727 <output name="anndata_out" ftype="h5ad">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
728 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
729 <has_h5_keys keys="var/highly_variable,var/means,var/dispersions,var/dispersions_norm"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
730 <has_h5_keys keys="uns/hvg"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
731 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
732 </output>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
733 </test>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
734
21
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
735 <!-- test 9 -->
11
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
736 <test expect_num_outputs="2">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
737 <param name="adata" value="krumsiek11.h5ad"/>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
738 <conditional name="method">
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
739 <param name="method" value="pp.subsample"/>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
740 <conditional name="type">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
741 <param name="type" value="fraction"/>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
742 <param name="fraction" value="0.5"/>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
743 </conditional>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
744 </conditional>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
745 <section name="advanced_common">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
746 <param name="show_log" value="true"/>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
747 </section>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
748 <assert_stdout>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
749 <has_text_matching expression="320 × 11"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
750 </assert_stdout>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
751 <output name="hidden_output">
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
752 <assert_contents>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
753 <has_text_matching expression="sc.pp.subsample"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
754 <has_text_matching expression="fraction=0.5"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
755 <has_text_matching expression="random_state=0"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
756 </assert_contents>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
757 </output>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
758 <output name="anndata_out" ftype="h5ad">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
759 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
760 <has_h5_keys keys="obs/cell_type"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
761 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
762 </output>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
763 </test>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
764
21
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
765 <!-- test 10 -->
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
766 <test expect_num_outputs="2">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
767 <param name="adata" value="krumsiek11.h5ad"/>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
768 <conditional name="method">
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
769 <param name="method" value="pp.subsample"/>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
770 <conditional name="type">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
771 <param name="type" value="n_obs"/>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
772 <param name="n_obs" value="10"/>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
773 </conditional>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
774 </conditional>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
775 <section name="advanced_common">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
776 <param name="show_log" value="true"/>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
777 </section>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
778 <assert_stdout>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
779 <has_text_matching expression="10 × 11"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
780 </assert_stdout>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
781 <output name="hidden_output">
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
782 <assert_contents>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
783 <has_text_matching expression="sc.pp.subsample"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
784 <has_text_matching expression="n_obs=10"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
785 <has_text_matching expression="random_state=0"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
786 </assert_contents>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
787 </output>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
788 <output name="anndata_out" ftype="h5ad">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
789 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
790 <has_h5_keys keys="obs/cell_type"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
791 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
792 </output>
1
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
793 </test>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
794
21
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
795 <!-- test 11 -->
11
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
796 <test expect_num_outputs="2">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
797 <param name="adata" value="random-randint.h5ad"/>
1
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
798 <conditional name="method">
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
799 <param name="method" value="pp.downsample_counts"/>
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
800 <param name="total_counts" value="20000"/>
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
801 </conditional>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
802 <section name="advanced_common">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
803 <param name="show_log" value="true"/>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
804 </section>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
805 <output name="hidden_output">
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
806 <assert_contents>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
807 <has_text_matching expression="sc.pp.downsample_counts"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
808 <has_text_matching expression="total_counts=20000"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
809 <has_text_matching expression="random_state=0"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
810 <has_text_matching expression="replace=False"/>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
811 <has_text_matching expression="Sum of total counts before: 49983776.0"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
812 <has_text_matching expression="Sum of total counts after: 20000"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
813 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
814 </output>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
815 <output name="anndata_out" ftype="h5ad">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
816 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
817 <has_h5_keys keys="var/index"/>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
818 </assert_contents>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
819 </output>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
820 </test>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
821
21
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
822 <!-- test 12 -->
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
823 <test expect_num_outputs="2">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
824 <param name="adata" value="random-randint.h5ad"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
825 <conditional name="method">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
826 <param name="method" value="pp.downsample_counts"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
827 <param name="counts_per_cell" value="20000"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
828 </conditional>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
829 <section name="advanced_common">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
830 <param name="show_log" value="true"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
831 </section>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
832 <output name="hidden_output">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
833 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
834 <has_text_matching expression="sc.pp.downsample_counts"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
835 <has_text_matching expression="counts_per_cell=20000"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
836 <has_text_matching expression="random_state=0"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
837 <has_text_matching expression="replace=False"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
838 <has_text_matching expression="Sum of counts for the first cell before: 489934.0"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
839 <has_text_matching expression="Sum of counts for the last cell before: 503669.0"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
840 <has_text_matching expression="Sum of counts for the first cell after: 20000.0"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
841 <has_text_matching expression="Sum of counts for the last cell after: 20000.0"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
842 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
843 </output>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
844 <output name="anndata_out" ftype="h5ad">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
845 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
846 <has_h5_keys keys="var/index"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
847 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
848 </output>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
849 </test>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
850
21
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
851 <!-- test 13 -->
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
852 <test expect_num_outputs="2">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
853 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad"/>
15
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
854 <conditional name="method">
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
855 <param name="method" value="filter_marker"/>
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
856 <param name="markerfile" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.tsv"/>
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
857 <param name="thresh_frac" value="0.2"/>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
858 <conditional name="layer_selection">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
859 <param name="use_raw" value="True"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
860 </conditional>
15
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
861 <param name="groupby" value="bulk_labels"/>
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
862 </conditional>
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
863 <section name="advanced_common">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
864 <param name="show_log" value="true"/>
15
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
865 </section>
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
866 <output name="hidden_output">
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
867 <assert_contents>
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
868 <has_text_matching expression="adata, key, x, 1.0, 0.2, 'bulk_labels'"/>
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
869 </assert_contents>
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
870 </output>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
871 <output name="marker_out" ftype="tabular">
15
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
872 <assert_contents>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
873 <has_text text="CD14+ Monocyte"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
874 <has_text text="C9orf142"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
875 <has_text text="EGR1"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
876 <has_text text="GZMB"/>
15
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
877 </assert_contents>
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
878 </output>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
879 </test>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
880
21
5b3c1679d29b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6
iuc
parents: 17
diff changeset
881 <!-- test 14 -->
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
882 <test expect_num_outputs="2">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
883 <param name="adata" value="krumsiek11.h5ad"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
884 <conditional name="method">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
885 <param name="method" value="pp.scrublet"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
886 <param name="n_prin_comps" value="5"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
887 </conditional>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
888 <section name="advanced_common">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
889 <param name="show_log" value="true"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
890 </section>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
891 <output name="hidden_output">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
892 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
893 <has_text_matching expression="sc.pp.scrublet"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
894 <has_text_matching expression="sim_doublet_ratio=2.0"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
895 <has_text_matching expression="expected_doublet_rate=0.05"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
896 <has_text_matching expression="n_prin_comps=5"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
897 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
898 </output>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
899 <output name="anndata_out" ftype="h5ad">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
900 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
901 <has_h5_keys keys="obs/doublet_score,obs/predicted_doublet"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
902 <has_h5_keys keys="uns/scrublet"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
903 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
904 </output>
15
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
905 </test>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
906 </tests>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
907 <help><![CDATA[
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
908
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
909 Filter cells outliers based on counts and numbers of genes expressed (`pp.filter_cells`)
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
910 ========================================================================================
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
911
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
912 For instance, only keep cells with at least `min_counts` counts or
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
913 `min_genes` genes expressed. This is to filter measurement outliers, i.e.,
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
914 "unreliable" observations.
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
915
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
916 Only provide one of the optional parameters `min_counts`, `min_genes`,
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
917 `max_counts`, `max_genes` per call.
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
918
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
919 More details on the `scanpy documentation
14
d636ce5cde16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
920 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.filter_cells.html>`__
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
921
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
922
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
923 Filter genes based on number of cells or counts (`pp.filter_genes`)
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
924 ===================================================================
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
925
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
926 Keep genes that have at least `min_counts` counts or are expressed in at
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
927 least `min_cells` cells or have at most `max_counts` counts or are expressed
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
928 in at most `max_cells` cells.
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
929
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
930 Only provide one of the optional parameters `min_counts`, `min_cells`,
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
931 `max_counts`, `max_cells` per call.
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
932
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
933 More details on the `scanpy documentation
14
d636ce5cde16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
934 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.filter_genes.html>`__
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
935
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
936
1
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
937 Filters out genes based on fold change and fraction of genes expressing the gene within and outside the groupby categories (`tl.filter_rank_genes_groups`)
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
938 ==========================================================================================================================================================
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
939
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
940 More details on the `scanpy documentation
14
d636ce5cde16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
941 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.filter_rank_genes_groups.html>`__
1
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
942
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
943
1
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
944 Annotate highly variable genes (`pp.highly_variable_genes`)
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
945 ===========================================================
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
946
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
947 It expects logarithmized data.
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
948
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
949 Depending on flavor, this reproduces the R-implementations of Seurat or Cell Ranger. The normalized dispersion is obtained by scaling with the mean and standard deviation of the dispersions for genes falling into a given bin for mean expression of genes. This means that for each bin of mean expression, highly variable genes are selected.
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
950
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
951
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
952 Subsample to a fraction of the number of observations (`pp.subsample`)
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
953 ======================================================================
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
954
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
955 More details on the `scanpy documentation
14
d636ce5cde16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
956 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.subsample.html>`__
1
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
957
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
958 Downsample counts (`pp.downsample_counts`)
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
959 ==========================================
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
960
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961 Downsample counts so that each cell has no more than `target_counts`. Cells with fewer counts than `target_counts` are unaffected by this. This
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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962 has been implemented by M. D. Luecken.
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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963
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964 More details on the `scanpy documentation
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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965 <https://scanpy.readthedocs.io/en/stable/generated/scanpy.pp.downsample_counts.html>`__
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966
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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967 Filter marker genes (`filter_marker`)
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968 =====================================
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969
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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970 This option is specific for celltype marker gene detection. You can generate a celltype marker gene file (tsv) with **COSG** provided at Galaxy.
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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971
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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972 The marker gene file should have as rows celltypes and columns as marker genes. Each celltype can have varying number of marker genes.
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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973
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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974 A marker gene is returned (retained in the list) if the mean expression of the marker gene is bigger than the threshold of mean expression (thresh_mean) and if the fraction of cells with the marker gene expression is equal or higher than the cell fraction threshold (thresh_frac).
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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975
1
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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976 More details on the `scanpy documentation
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977 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.downsample_counts.html>`__
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978
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979
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980 Predict cell doublets using a nearest-neighbor classifier of observed transcriptomes and simulated doublets. (`pp.scrublet`)
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981 ============================================================================================================================
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982
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983 Works best if the input is a raw (unnormalized) counts matrix from a single sample or a collection of similar samples from the same experiment. This function is a wrapper around functions that pre-process using Scanpy and directly call functions of Scrublet().
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984
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985 More details on the `scanpy documentation
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986 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.scrublet.html>`__
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987
0
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988 ]]></help>
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989 <expand macro="citations"/>
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990 </tool>