Mercurial > repos > iuc > scanpy_inspect
annotate inspect.xml @ 20:d86cb2ce311b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
author | iuc |
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date | Fri, 18 Oct 2024 10:39:04 +0000 |
parents | d1cd8c147809 |
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rev | line source |
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18
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
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1 <tool id="scanpy_inspect" name="Scanpy Inspect and manipulate" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> |
0
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
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2 <macros> |
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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3 <import>macros.xml</import> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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4 <xml name="params_score_genes"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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changeset
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5 <param argument="n_bins" type="integer" value="25" label="Number of expression level bins for sampling"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
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6 <param argument="random_state" type="integer" value="0" label="Random seed for sampling"/> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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7 <expand macro="param_use_raw"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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8 </xml> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
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9 <token name="@CMD_PARAMS_SCORE_GENES@"><![CDATA[ |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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changeset
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10 n_bins=$method.n_bins, |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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11 random_state=$method.random_state, |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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12 use_raw=$method.use_raw, |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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13 copy=False |
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18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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14 ]]> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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15 </token> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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16 <xml name="corr_method"> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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17 <param argument="corr_method" type="select" label="P-value correction method"> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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18 <option value="benjamini-hochberg" selected="true">Benjamini-Hochberg</option> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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19 <option value="bonferroni">Bonferroni</option> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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20 </param> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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21 </xml> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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22 <xml name="fit_intercept"> |
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18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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23 <param argument="fit_intercept" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Should a constant (a.k.a. bias or intercept) be added to the decision function?"/> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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24 </xml> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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25 <xml name="max_iter"> |
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18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
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26 <param argument="max_iter" type="integer" min="0" value="100" label="Maximum number of iterations taken for the solvers to converge"/> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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27 </xml> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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28 <xml name="multi_class"> |
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18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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29 <param argument="multi_class" type="select" label="Multi class"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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30 <option value="auto" selected="true">auto: selects ‘ovr’ if the data is binary and otherwise selects ‘multinomial’</option> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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31 <option value="ovr">ovr: a binary problem is fit for each label</option> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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32 <option value="multinomial">multinomial: the multinomial loss fit across the entire probability distribution, even when the data is binary</option> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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33 </param> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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34 </xml> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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35 <xml name="penalty"> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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36 <param argument="penalty" type="select" label="Norm used in the penalization"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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37 <option value="l2" selected="true">l2</option> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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38 <option value="l1">l1</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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39 <yield/> |
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6c145a6868cc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
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40 </param> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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41 </xml> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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42 <xml name="random_state"> |
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18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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43 <param argument="random_state" type="integer" value="" optional="true" label="The seed of the pseudo random number generator to use when shuffling the data"/> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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44 </xml> |
0
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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45 </macros> |
11
6bd82ed14acd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
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46 <expand macro="bio_tools"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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47 <expand macro="requirements"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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48 <requirement type="package" version="1.5.1">scikit-learn</requirement> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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49 </expand> |
0
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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50 <expand macro="version_command"/> |
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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51 <command detect_errors="exit_code"><![CDATA[ |
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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52 @CMD@ |
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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53 ]]></command> |
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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54 <configfiles> |
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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55 <configfile name="script_file"><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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56 @CMD_IMPORTS@ |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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57 @CMD_READ_INPUTS@ |
0
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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58 |
17
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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59 #if str($method.method) == 'pp.calculate_qc_metrics': |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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60 sc.pp.calculate_qc_metrics( |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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61 adata=adata, |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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62 expr_type='$method.expr_type', |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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63 var_type='$method.var_type', |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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64 #if str($method.qc_vars) != '': |
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a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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65 #set $qc_vars = [str(x.strip()) for x in str($method.qc_vars).split(',')] |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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66 qc_vars=$qc_vars, |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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67 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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68 #if str($method.percent_top) != '': |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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69 #set $percent_top = [int(x.strip()) for x in str($method.percent_top).split(',')] |
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18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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70 percent_top=$percent_top, |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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71 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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72 #if str($method.layer) != '': |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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73 layer='$method.layer', |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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74 #end if |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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75 use_raw=$method.use_raw, |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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76 log1p=$method.log1p, |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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77 inplace=True) |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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78 |
17
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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79 #else if str($method.method) == 'pp.neighbors': |
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80 sc.pp.neighbors( |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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81 adata=adata, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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82 n_neighbors=$method.n_neighbors, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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83 #if str($method.n_pcs) != '': |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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84 n_pcs=$method.n_pcs, |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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85 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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86 #if str($method.use_rep) != '': |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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87 use_rep='$method.use_rep', |
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88 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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89 knn=$method.knn, |
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90 method='$method.pp_neighbors_method', |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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91 metric='$method.metric', |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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92 random_state=$method.random_state, |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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93 #if str($method.key_added) != '': |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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94 key_added='$method.key_added', |
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95 #end if |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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96 copy=False) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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97 |
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98 #else if str($method.method) == 'tl.score_genes': |
1
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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99 sc.tl.score_genes( |
0
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100 adata=adata, |
1
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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101 #set $gene_list = [str(x.strip()) for x in str($method.gene_list).split(',')] |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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102 gene_list=$gene_list, |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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103 ctrl_size=$method.ctrl_size, |
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104 #if str($method.gene_pool) != '': |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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105 #set $gene_pool = [str(x.strip()) for x in str($method.gene_pool).split(',')] |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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106 gene_pool=$gene_pool, |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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107 #end if |
17
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108 score_name='$method.score_name', |
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109 @CMD_PARAMS_SCORE_GENES@) |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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110 |
17
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111 #else if str($method.method) == 'tl.score_genes_cell_cycle': |
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112 #if str($method.s_genes.format) == 'file': |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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113 with open('$method.s_genes.file', 'r') as s_genes_f: |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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114 s_genes = [str(x.strip()) for x in s_genes_f.readlines()] |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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115 print(s_genes) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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116 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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117 |
17
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118 #if str($method.g2m_genes.format) == 'file': |
1
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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119 with open('$method.g2m_genes.file', 'r') as g2m_genes_f: |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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120 g2m_genes = [str(x.strip()) for x in g2m_genes_f.readlines()] |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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121 print(g2m_genes) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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122 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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123 |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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124 sc.tl.score_genes_cell_cycle( |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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125 adata=adata, |
17
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126 #if str($method.s_genes.format) == 'text': |
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127 #set $s_genes = [str(x.strip()) for x in str($method.s_genes.text).split(',')] |
1
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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128 s_genes=$s_genes, |
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129 #else if str($method.s_genes.format) == 'file': |
1
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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130 s_genes=s_genes, |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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131 #end if |
17
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132 #if str($method.g2m_genes.format) == 'text': |
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133 #set $g2m_genes = [str(x.strip()) for x in str($method.g2m_genes.text).split(',')] |
1
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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134 g2m_genes=$g2m_genes, |
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135 #else if str($method.g2m_genes.format) == 'file': |
1
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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136 g2m_genes=g2m_genes, |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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137 #end if |
17
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138 @CMD_PARAMS_SCORE_GENES@) |
1
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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139 |
17
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140 #else if str($method.method) == 'tl.rank_genes_groups': |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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141 sc.tl.rank_genes_groups( |
0
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142 adata=adata, |
17
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143 #if str($method.groupby) != '': |
1
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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144 groupby='$method.groupby', |
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145 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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146 use_raw=$method.use_raw, |
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147 #if str($method.groups) != '': |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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148 #set $group=[x.strip() for x in str($method.groups).split(',')] |
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149 groups=$group, |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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150 #end if |
17
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151 #if str($method.layer) != '': |
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152 layer='$method.layer', |
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153 #end if |
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154 #if str($method.ref.rest) == 'rest': |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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155 reference='$method.ref.rest', |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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156 #else |
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157 reference='$method.ref.reference', |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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158 #end if |
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159 #if str($method.n_genes) != '': |
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160 n_genes=$method.n_genes, |
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161 #end if |
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162 method='$method.tl_rank_genes_groups_method.method', |
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163 #if str($method.tl_rank_genes_groups_method.method) != 'logreg': |
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164 corr_method='$method.tl_rank_genes_groups_method.corr_method', |
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165 #end if |
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166 #if str($method.tl_rank_genes_groups_method.method) == 'wilcoxon': |
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167 tie_correct=$method.tl_rank_genes_groups_method.tie_correct, |
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168 #end if |
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169 #if str($method.tl_rank_genes_groups_method.method) == 'logreg': |
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170 solver='$method.tl_rank_genes_groups_method.solver.solver', |
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171 #if str($method.tl_rank_genes_groups_method.solver.solver) == 'lbfgs': |
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172 penalty='$method.tl_rank_genes_groups_method.solver.penalty', |
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173 fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept, |
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174 max_iter=$method.tl_rank_genes_groups_method.solver.max_iter, |
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175 multi_class='$method.tl_rank_genes_groups_method.solver.multi_class', |
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176 #else if str($method.tl_rank_genes_groups_method.solver.solver) == 'newton-cg': |
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177 penalty='$method.tl_rank_genes_groups_method.solver.penalty', |
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178 fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept, |
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179 max_iter=$method.tl_rank_genes_groups_method.solver.max_iter, |
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180 multi_class='$method.tl_rank_genes_groups_method.solver.multi_class', |
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181 #else if str($method.tl_rank_genes_groups_method.solver.solver) == 'liblinear': |
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182 #if str($method.tl_rank_genes_groups_method.solver.penalty.penalty) == 'l1': |
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183 penalty='l1', |
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184 #else: |
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185 penalty='l2', |
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186 dual=$method.tl_rank_genes_groups_method.solver.penalty.dual, |
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187 #end if |
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188 fit_intercept=$method.tl_rank_genes_groups_method.solver.intercept_scaling.fit_intercept, |
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189 #if str($method.tl_rank_genes_groups_method.solver.intercept_scaling.fit_intercept) == 'True': |
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190 intercept_scaling=$method.tl_rank_genes_groups_method.solver.intercept_scaling.intercept_scaling, |
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191 #end if |
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192 #if str($method.tl_rank_genes_groups_method.solver.random_state) != '': |
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193 random_state=$method.tl_rank_genes_groups_method.solver.random_state, |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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194 #end if |
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195 #else if str($method.tl_rank_genes_groups_method.solver.solver) == 'sag': |
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196 penalty='$method.tl_rank_genes_groups_method.solver.penalty.penalty', |
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197 fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept, |
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198 #if str($method.tl_rank_genes_groups_method.solver.random_state) != '': |
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199 random_state=$method.tl_rank_genes_groups_method.solver.random_state, |
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200 #end if |
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201 max_iter=$method.tl_rank_genes_groups_method.solver.max_iter, |
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202 multi_class=$method.tl_rank_genes_groups_method.solver.multi_class, |
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203 #else if str($method.tl_rank_genes_groups_method.solver.solver) == 'saga': |
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204 #if str($method.tl_rank_genes_groups_method.solver.penalty.penalty) == 'l1': |
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205 penalty='l1', |
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206 #else if str($method.tl_rank_genes_groups_method.solver.penalty.penalty) == 'l2': |
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207 penalty='l2', |
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208 #else if str($method.tl_rank_genes_groups_method.solver.penalty.penalty) == 'elasticnet': |
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209 penalty='elasticnet', |
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210 #else: |
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211 penalty='None', |
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212 #end if |
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213 fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept, |
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214 multi_class=$method.tl_rank_genes_groups_method.solver.multi_class, |
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215 #end if |
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216 tol=$method.tl_rank_genes_groups_method.tol, |
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217 C=$method.tl_rank_genes_groups_method.c, |
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218 #end if |
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219 #if str($method.key_added) != '': |
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220 key_added='$method.key_added', |
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221 #end if |
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222 copy=False) |
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223 |
20
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224 #if str($method.get_df.get_df_select) == 'True': |
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225 cluster_DEG = sc.get.rank_genes_groups_df(adata, |
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226 group=None, # return all groups |
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227 #if str($method.get_df.key) != '': |
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228 key='$method.get_df.key', |
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229 #end if |
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230 #if str($method.get_df.pval_cutoff) != '': |
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231 pval_cutoff=$method.get_df.pval_cutoff, |
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232 #end if |
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233 #if str($method.get_df.log2fc_min) != '': |
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234 log2fc_min=$method.get_df.log2fc_min, |
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235 #end if |
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236 #if str($method.get_df.log2fc_max) != '': |
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237 log2fc_max=$method.get_df.log2fc_max, |
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238 #end if |
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239 @CMD_PARAM_GENE_SYMBOLS@ |
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240 ) |
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241 |
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242 cluster_DEG.to_csv('DEG.tsv', sep="\t", index=False) |
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243 #end if |
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244 |
17
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245 #else if str($method.method) == "tl.marker_gene_overlap": |
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246 reference_markers = {} |
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247 #for $i, $s in enumerate($method.reference_markers) |
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248 #set $list=[x.strip() for x in str($s.values).split(',')] |
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249 reference_markers['$s.key'] = $list |
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250 #end for |
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251 |
17
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252 # Temporary fix for the issue with "inplace=True" for Pandas dataframes. |
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253 # see here: https://github.com/scverse/scanpy/blob/b6193502e11b84fc1b4a011ee9cf08a19da22ebf/src/scanpy/tools/_marker_gene_overlap.py#L167 |
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254 marker_overlap_result = sc.tl.marker_gene_overlap( |
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255 adata, |
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256 reference_markers, |
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257 #if str($method.key) != '': |
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258 key='$method.key', |
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259 #end if |
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260 method='$method.overlap.method', |
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261 #if str($method.overlap.method) == 'overlap_count' and str($method.overlap.normalize) != 'None': |
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262 normalize='$method.overlap.normalize', |
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263 #end if |
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264 #if str($method.top_n_markers) != '': |
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265 top_n_markers=$method.top_n_markers, |
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266 #end if |
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267 #if str($method.adj_pval_threshold) != '': |
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268 adj_pval_threshold=$method.adj_pval_threshold, |
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269 #end if |
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270 #if $method.key_added: |
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271 key_added='$method.key_added', |
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272 #end if |
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273 inplace=False) |
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274 |
17
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275 adata.uns['marker_gene_overlap'] = marker_overlap_result |
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276 |
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277 #else if str($method.method) == "pp.log1p": |
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278 sc.pp.log1p( |
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279 adata, |
17
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280 #if str($method.base) != '': |
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281 base=$method.base, |
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282 #end if |
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283 #if str($method.layer) != '': |
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284 layer='$method.layer', |
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285 #end if |
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286 #if str($method.obsm) != '': |
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287 obsm='$method.obsm', |
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288 #end if |
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289 copy=False) |
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290 |
17
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291 #else if str($method.method) == "pp.scale": |
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292 sc.pp.scale( |
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293 adata, |
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294 zero_center=$method.zero_center, |
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295 #if str($method.max_value) != '': |
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296 max_value=$method.max_value, |
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297 #end if |
17
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298 #if str($method.layer) != '': |
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299 layer='$method.layer', |
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300 #end if |
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301 #if str($method.obsm) != '': |
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302 obsm='$method.obsm', |
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303 #end if |
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304 #if str($method.mask_obs) != '': |
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305 mask_obs='$method.mask_obs', |
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306 #end if |
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307 copy=False) |
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308 |
17
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309 #else if str($method.method) == "pp.sqrt": |
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310 |
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311 print("stats before sqrt:", "min=", adata.X.min(), "max=", adata.X.max(), "mean=", adata.X.mean()) |
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312 |
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313 sc.pp.sqrt( |
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314 adata, |
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315 copy=False) |
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316 |
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317 print("stats after sqrt:", "min=", adata.X.min(), "max=", adata.X.max(), "mean=", adata.X.mean()) |
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318 #end if |
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319 |
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320 @CMD_ANNDATA_WRITE_OUTPUTS@ |
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321 ]]> |
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322 </configfile> |
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323 </configfiles> |
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324 <inputs> |
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325 <expand macro="inputs_anndata"/> |
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326 <conditional name="method"> |
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327 <param argument="method" type="select" label="Method used for inspecting"> |
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328 <option value="pp.calculate_qc_metrics">Calculate quality control metrics, using 'pp.calculate_qc_metrics'</option> |
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329 <option value="pp.neighbors">Compute a neighborhood graph of observations, using 'pp.neighbors'</option> |
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330 <option value="tl.score_genes">Score a set of genes, using 'tl.score_genes'</option> |
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331 <option value="tl.score_genes_cell_cycle">Score cell cycle genes, using 'tl.score_genes_cell_cycle'</option> |
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332 <option value="tl.rank_genes_groups">Rank genes for characterizing groups, using 'tl.rank_genes_groups'</option> |
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333 <option value="tl.marker_gene_overlap">Calculate an overlap score between data-deriven marker genes and provided markers, using 'tl.marker_gene_overlap'</option> |
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334 <option value="pp.log1p">Logarithmize the data matrix, using 'pp.log1p'</option> |
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335 <option value="pp.scale">Scale data to unit variance and zero mean, using 'pp.scale'</option> |
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336 <option value="pp.sqrt">Square root the data matrix, using 'pp.sqrt'</option> |
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337 </param> |
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338 <when value="pp.calculate_qc_metrics"> |
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339 <param argument="expr_type" type="text" value="counts" label="Name of kind of values in X"> |
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340 <expand macro="sanitize_query"/> |
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341 </param> |
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342 <param argument="var_type" type="text" value="genes" label="The kind of thing the variables are"> |
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343 <expand macro="sanitize_query"/> |
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344 </param> |
17
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345 <param argument="qc_vars" type="text" optional="true" value="" label="Keys for boolean columns of '.var' which identify variables you could want to control for" help="Keys separated by a comma"> |
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346 <expand macro="sanitize_query"/> |
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347 </param> |
17
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348 <param argument="percent_top" type="text" value="" optional="true" label="Proportions of top genes to cover" |
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349 help=" Values (integers) are considered 1-indexed, '50' finds cumulative proportion to the 50th most expressed genes. Values separated by a comma. If empty don't calculate"> |
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350 <expand macro="sanitize_vectors"/> |
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351 </param> |
17
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352 <expand macro="param_layer"/> |
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353 <expand macro="param_use_raw"/> |
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354 <param argument="log1p" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Compute log1p transformed annotations"/> |
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355 </when> |
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356 <when value="pp.neighbors"> |
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357 <param argument="n_neighbors" type="integer" min="0" value="15" label="The size of local neighborhood (in terms of number of neighboring data points) used for manifold approximation" help="Larger values result in more global views of the manifold, while smaller values result in more local data being preserved. In general values should be in the range 2 to 100. If 'knn' is 'True', number of nearest neighbors to be searched. If 'knn' is 'False', a Gaussian kernel width is set to the distance of the 'n_neighbors' neighbor."/> |
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358 <param argument="n_pcs" type="integer" min="0" value="" optional="true" label="Number of PCs to use"/> |
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359 <expand macro="param_use_rep"/> |
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360 <param argument="knn" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Use a hard threshold to restrict the number of neighbors to n_neighbors?" help="If true, it considers a knn graph. Otherwise, it uses a Gaussian Kernel to assign low weights to neighbors more distant than the 'n_neighbors' nearest neighbor."/> |
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361 <param name="pp_neighbors_method" argument="method" type="select" label="Method for computing connectivities"> |
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362 <option value="umap" selected="true">umap (McInnes et al, 2018)</option> |
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363 <option value="gauss">gauss: Gauss kernel following (Coifman et al 2005) with adaptive width (Haghverdi et al 2016)</option> |
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364 </param> |
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365 <param argument="metric" type="select" label="Distance metric"> |
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366 <expand macro="distance_metric_options"/> |
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367 </param> |
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368 <param argument="random_state" type="integer" value="0" label="Numpy random seed"/> |
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369 <param argument="key_added" type="text" value="" optional="true" label="Key to store neighbors, distances and connectivities" help="If specified, the neighbors data is added to .uns[key_added], distances are stored in .obsp[key_added+'_distances'] and connectivities in .obsp[key_added+'_connectivities']"/> |
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370 </when> |
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371 <when value="tl.score_genes"> |
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372 <param argument="gene_list" type="text" value="" optional="false" label="The list of gene names used for score calculation" help="Genes separated by a comma"> |
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373 <expand macro="sanitize_query"/> |
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374 </param> |
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375 <param argument="ctrl_size" type="integer" value="50" label="Number of reference genes to be sampled" help="If 'len(gene_list)' is not too low, you can set 'ctrl_size=len(gene_list)'."/> |
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376 <param argument="gene_pool" type="text" value="" optional="true" label="Genes for sampling the reference set" help="Default is all genes. Genes separated by a comma"> |
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377 <expand macro="sanitize_query"/> |
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378 </param> |
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379 <param argument="score_name" type="text" value="score" label="Name of the field to be added in '.obs'"> |
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380 <expand macro="sanitize_query"/> |
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381 </param> |
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382 <expand macro="params_score_genes"/> |
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383 </when> |
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384 <when value="tl.score_genes_cell_cycle"> |
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385 <conditional name='s_genes'> |
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diff
changeset
|
386 <param name="format" type="select" label="Format for the list of genes associated with S phase"> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
387 <option value="text" selected="true">Text</option> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
388 <option value="file">File</option> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
389 </param> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
390 <when value="text"> |
7
6c145a6868cc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
parents:
6
diff
changeset
|
391 <param name="text" type="text" value="" label="List of genes associated with S phase" help="Genes separated by a comma"> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
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|
392 <expand macro="sanitize_query"/> |
7
6c145a6868cc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
parents:
6
diff
changeset
|
393 </param> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
394 </when> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
395 <when value="file"> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
396 <param name="file" type="data" format="txt" label="File with the list of genes associated with S phase" help="One gene per line"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
397 </when> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
398 </conditional> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
399 <conditional name='g2m_genes'> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
400 <param name="format" type="select" label="Format for the list of genes associated with G2M phase"> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
401 <option value="text" selected="true">Text</option> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
402 <option value="file">File</option> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
403 </param> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
404 <when value="text"> |
7
6c145a6868cc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
parents:
6
diff
changeset
|
405 <param name="text" type="text" value="" label="List of genes associated with G2M phase" help="Genes separated by a comma"> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
406 <expand macro="sanitize_query"/> |
7
6c145a6868cc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
parents:
6
diff
changeset
|
407 </param> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
408 </when> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
409 <when value="file"> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
410 <param name="file" type="data" format="txt" label="File with the list of genes associated with G2M phase" help="One gene per line"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
411 </when> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
412 </conditional> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
413 <expand macro="params_score_genes"/> |
0
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
414 </when> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
415 <when value="tl.rank_genes_groups"> |
20
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
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diff
changeset
|
416 <conditional name="get_df"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
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diff
changeset
|
417 <param name="get_df_select" type="select" label="Get ranked genes as a Tabular file?"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
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diff
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418 <option value="False" selected="true">False</option> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
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diff
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419 <option value="True">True</option> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
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diff
changeset
|
420 </param> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
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diff
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|
421 <when value="False"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
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diff
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422 <when value="True"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
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diff
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|
423 <param argument="key" type="text" value="" optional="true" label="Key differential expression groups were stored under"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
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diff
changeset
|
424 <param argument="pval_cutoff" type="float" min="0.0" value="" optional="true" label="Return only adjusted p-values below the cutoff."/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
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diff
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|
425 <param argument="log2fc_min" type="float" value="" optional="true" label="Minimum logfc to return."/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
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diff
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|
426 <param argument="log2fc_max" type="float" value="" optional="true" label="Maximum logfc to return."/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
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|
427 <expand macro="param_gene_symbols" label="Column name in [.var] DataFrame that stores gene symbols."/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
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diff
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428 </when> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
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|
429 </conditional> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
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|
430 <param argument="groupby" type="text" value="" label="The key of the observations grouping to consider"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
431 <expand macro="sanitize_query"/> |
7
6c145a6868cc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
parents:
6
diff
changeset
|
432 </param> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
433 <expand macro="param_use_raw"/> |
7
6c145a6868cc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
parents:
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diff
changeset
|
434 <param argument="groups" type="text" value="" label="Subset of groups to which comparison shall be restricted" help="e.g. ['g1', 'g2', 'g3']. If not passed, a ranking will be generated for all groups."> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
435 <expand macro="sanitize_query"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
436 </param> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
437 <param argument="layer" type="text" value="" label="Key from adata.layers whose value will be used to perform tests on"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
438 <expand macro="sanitize_query"/> |
7
6c145a6868cc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
parents:
6
diff
changeset
|
439 </param> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
440 <conditional name="ref"> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
441 <param name="rest" type="select" label="Comparison"> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
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|
442 <option value="rest" selected="true">Compare each group to the union of the rest of the group</option> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
443 <option value="group_id">Compare with respect to a specific group</option> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
444 </param> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
445 <when value="rest"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
446 <when value="group_id"> |
7
6c145a6868cc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
parents:
6
diff
changeset
|
447 <param argument="reference" type="text" value="" label="Group identifier with respect to which compare"> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
448 <expand macro="sanitize_query"/> |
7
6c145a6868cc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
iuc
parents:
6
diff
changeset
|
449 </param> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
450 </when> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
451 </conditional> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
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|
452 <param argument="n_genes" type="integer" min="0" value="" optional="true" label="The number of genes that appear in the returned tables" help="Defaults to all genes"/> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
453 <conditional name="tl_rank_genes_groups_method"> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
454 <param argument="method" type="select" label="Method"> |
12
3081ff5c84a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0
iuc
parents:
11
diff
changeset
|
455 <option value="t-test" selected="true">t-test</option> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
456 <option value="wilcoxon">Wilcoxon-Rank-Sum</option> |
12
3081ff5c84a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0
iuc
parents:
11
diff
changeset
|
457 <option value="t-test_overestim_var">t-test with overestimate of variance of each group</option> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
458 <option value="logreg">Logistic regression</option> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
459 </param> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
460 <when value="t-test"> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
461 <expand macro="corr_method"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
462 </when> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
463 <when value="wilcoxon"> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
464 <expand macro="corr_method"/> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
465 <param argument="tie_correct" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use tie correction for 'wilcoxon' scores"/> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
466 </when> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
467 <when value="t-test_overestim_var"> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
468 <expand macro="corr_method"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
469 </when> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
470 <when value="logreg"> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
471 <conditional name="solver"> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
472 <param argument="solver" type="select" label="Algorithm to use in the optimization problem" help="For small datasets, ‘liblinear’ is a good choice, whereas ‘sag’ and ‘saga’ are faster for large ones. For multiclass problems, only ‘newton-cg’, ‘sag’, ‘saga’ and ‘lbfgs’ handle multinomial loss; ‘liblinear’ is limited to one-versus-rest schemes. ‘newton-cg’, ‘lbfgs’ and ‘sag’ only handle L2 penalty, whereas ‘liblinear’ and ‘saga’ handle L1 penalty."> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
473 <option value="lbfgs" selected="true">lbfgs</option> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
474 <option value="newton-cg">newton-cg</option> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
475 <option value="liblinear">liblinear</option> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
476 <option value="sag">sag</option> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
477 <option value="saga">saga</option> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
478 </param> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
479 <when value="lbfgs"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
480 <param name="penalty" type="boolean" truevalue="l2" falsevalue="None" checked="true" label="use l2 penalty?"/> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
481 <expand macro="fit_intercept"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
482 <expand macro="max_iter"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
483 <expand macro="multi_class"/> |
18
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
484 </when> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
485 <when value="newton-cg"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
486 <param name="penalty" type="boolean" truevalue="l2" falsevalue="None" checked="true" label="use l2 penalty?"/> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
487 <expand macro="fit_intercept"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
488 <expand macro="max_iter"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
489 <expand macro="multi_class"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
490 </when> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
491 <when value="liblinear"> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
492 <conditional name="penalty"> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
493 <expand macro="penalty"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
494 <when value="l1"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
495 <when value="l2"> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
496 <param argument="dual" type="boolean" truevalue="True" falsevalue="False" checked="false" |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
497 label="Dual (not primal) formulation?" help="Prefer primal when n_samples > n_features"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
498 </when> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
499 </conditional> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
500 <conditional name="intercept_scaling"> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
501 <param argument="fit_intercept" type="select" label="Should a constant (a.k.a. bias or intercept) be added to the decision function?"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
502 <option value="True" selected="true">Yes</option> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
503 <option value="False">No</option> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
504 </param> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
505 <when value="True"> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
506 <param argument="intercept_scaling" type="float" value="1.0" label="Intercept scaling" help="x becomes [x, self.intercept_scaling], i.e. a 'synthetic' feature with constant value equal to intercept_scaling is appended to the instance vector. The intercept becomes intercept_scaling * synthetic_feature_weight."/> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
507 </when> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
508 <when value="False"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
509 </conditional> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
510 <expand macro="random_state"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
511 </when> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
512 <when value="sag"> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
513 <param name="penalty" type="boolean" truevalue="l2" falsevalue="None" checked="true" label="use l2 penalty?"/> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
514 <expand macro="fit_intercept"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
515 <expand macro="random_state"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
516 <expand macro="max_iter"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
517 <expand macro="multi_class"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
518 </when> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
519 <when value="saga"> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
520 <conditional name="penalty"> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
521 <expand macro="penalty"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
522 <option value="elasticnet">elasticnet</option> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
523 <option value="None">None</option> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
524 </expand> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
525 <when value="l1"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
526 <when value="l2"/> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
527 <when value="elasticnet"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
528 <when value="None"/> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
529 </conditional> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
530 <expand macro="fit_intercept"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
531 <expand macro="multi_class"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
532 </when> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
533 </conditional> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
534 <param argument="tol" type="float" value="1e-4" label="Tolerance for stopping criteria"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
535 <param argument="c" type="float" value="1.0" label="Inverse of regularization strength" help="It must be a positive float. Like in support vector machines, smaller values specify stronger regularization."/> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
536 </when> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
537 </conditional> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
538 <param argument="key_added" type="text" value="" optional="true" label="The key in adata.uns information is saved to"/> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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|
539 </when> |
11
6bd82ed14acd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
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changeset
|
540 <!-- With inplace=True, NotImplementedError: Writing Pandas dataframes to h5ad is currently under development. Please use `inplace=False`. --> |
17
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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changeset
|
541 <!-- Issue is fixed in the script --> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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542 <when value="tl.marker_gene_overlap"> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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changeset
|
543 <repeat name="reference_markers" title="Marker genes"> |
17
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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544 <param name="key" type="text" value="" label="Cell identity name"/> |
3
cc0deb593fc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents:
2
diff
changeset
|
545 <param name="values" type="text" value="" label="List of genes" help="Comma-separated names from 'var'"/> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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changeset
|
546 </repeat> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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changeset
|
547 <param argument="key" type="text" value="rank_genes_groups" label="Key in adata.uns where the rank_genes_groups output is stored"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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|
548 <conditional name="overlap"> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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changeset
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549 <param argument="method" type="select" label="Method to calculate marker gene overlap"> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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diff
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550 <option value="overlap_count" selected="true">overlap_count: Intersection of the gene set</option> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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|
551 <option value="overlap_coef">overlap_coef: Overlap coefficient</option> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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552 <option value="jaccard">jaccard: Jaccard index</option> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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553 </param> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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diff
changeset
|
554 <when value="overlap_count"> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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diff
changeset
|
555 <param argument="normalize" type="select" label="Normalization option for the marker gene overlap output"> |
17
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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diff
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|
556 <option value="None" selected="true">None</option> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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diff
changeset
|
557 <option value="reference">reference: Normalization of the data by the total number of marker genes given in the reference annotation per group</option> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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|
558 <option value="data">data: Normalization of the data by the total number of marker genes used for each cluster</option> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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|
559 </param> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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560 </when> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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diff
changeset
|
561 <when value="overlap_coef"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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diff
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|
562 <when value="jaccard"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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563 </conditional> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
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564 <param argument="top_n_markers" type="integer" optional="true" value="" label="Number of top data-derived marker genes to use" help="By default all calculated marker genes are used. If adj_pval_threshold is set along with top_n_markers, then adj_pval_threshold is ignored."/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents:
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diff
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|
565 <param argument="adj_pval_threshold" type="float" optional="true" value="" label="Significance threshold on the adjusted p-values to select marker genes" help=" This can only be used when adjusted p-values are calculated by 'tl.rank_genes_groups'. If adj_pval_threshold is set along with top_n_markers, then adj_pval_threshold is ignored."/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents:
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diff
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|
566 <param argument="key_added" type="text" optional="true" value="" label="Key that will contain the marker overlap scores in 'uns'"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
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|
567 </when> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
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568 <when value="pp.log1p"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
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|
569 <param argument="base" type="integer" value="" optional="true" label="Base of the logarithm." help="Natural logarithm is used by default."/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
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|
570 <param argument="layer" type="text" value="" optional="true" label="Entry of layers to transform"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
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|
571 <expand macro="sanitize_query"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents:
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diff
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|
572 </param> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
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|
573 <param argument="obsm" type="text" value="" optional="true" label="Entry of obsm to transform"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
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|
574 <expand macro="sanitize_query"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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diff
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|
575 </param> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
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|
576 </when> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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diff
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|
577 <when value="pp.scale"> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents:
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diff
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578 <param argument="zero_center" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Zero center?" help="If not, it omits zero-centering variables, which allows to handle sparse input efficiently."/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents:
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|
579 <param argument="max_value" type="float" value="" optional="true" label="Maximum value" help="Clip (truncate) to this value after scaling. If not set, it does not clip."/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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580 <param argument="layer" type="text" value="" label="Which element of layers to scale"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
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|
581 <expand macro="sanitize_query"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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|
582 </param> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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|
583 <param argument="obsm" type="text" value="" label="Which element of obsm to scale"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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|
584 <expand macro="sanitize_query"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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|
585 </param> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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586 <param argument="mask_obs" type="text" value="" label="Restrict both the derivation of scaling parameters and the scaling itself to a certain set of observations."> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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587 <expand macro="sanitize_query"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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588 </param> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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589 </when> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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590 <when value="pp.sqrt"/> |
0
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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591 </conditional> |
6
5e9171dc8244
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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592 <expand macro="inputs_common_advanced"/> |
0
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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593 </inputs> |
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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594 <outputs> |
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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595 <expand macro="anndata_outputs"/> |
20
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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596 <data name="ranked_gene" format="tabular" from_work_dir="DEG.tsv" label="${tool.name} (${method.method}) on ${on_string}: Ranked genes"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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597 <filter> method['method'] == 'tl.rank_genes_groups' and method['get_df']['get_df_select'] == 'True'</filter> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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598 </data> |
0
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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599 </outputs> |
5d2e17328afe
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600 <tests> |
18
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601 <!-- test 1 --> |
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602 <test expect_num_outputs="2"> |
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603 <param name="adata" value="sparce_csr_matrix.h5ad"/> |
0
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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604 <conditional name="method"> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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605 <param name="method" value="pp.calculate_qc_metrics"/> |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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606 <param name="qc_vars" value="mito,negative"/> |
0
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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607 </conditional> |
6
5e9171dc8244
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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|
608 <section name="advanced_common"> |
17
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609 <param name="show_log" value="true"/> |
6
5e9171dc8244
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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610 </section> |
5e9171dc8244
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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611 <output name="hidden_output"> |
5e9171dc8244
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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|
612 <assert_contents> |
17
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613 <has_text_matching expression="sc.pp.calculate_qc_metrics"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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614 <has_text_matching expression="expr_type='counts'"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
615 <has_text_matching expression="var_type='genes'"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
616 <has_text_matching expression="qc_vars=\['mito', 'negative'\]"/> |
6
5e9171dc8244
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
617 </assert_contents> |
5e9171dc8244
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
618 </output> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
619 <output name="anndata_out" ftype="h5ad"> |
6
5e9171dc8244
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents:
5
diff
changeset
|
620 <assert_contents> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
621 <has_h5_keys keys="obs/n_genes_by_counts,obs/log1p_n_genes_by_counts,obs/total_counts,obs/log1p_total_counts,obs/pct_counts_in_top_50_genes,obs/pct_counts_in_top_100_genes,obs/pct_counts_in_top_200_genes,obs/pct_counts_in_top_500_genes,obs/total_counts_mito,obs/log1p_total_counts_mito,obs/pct_counts_mito,obs/total_counts_negative,obs/log1p_total_counts_negative,obs/pct_counts_negative"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
622 <has_h5_keys keys="var/n_cells_by_counts,var/mean_counts,var/log1p_mean_counts,var/pct_dropout_by_counts,var/total_counts,var/log1p_total_counts"/> |
0
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
623 </assert_contents> |
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
624 </output> |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
625 </test> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
626 |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
627 <!-- test 2 --> |
11
6bd82ed14acd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents:
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diff
changeset
|
628 <test expect_num_outputs="2"> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
629 <param name="adata" value="sparce_csr_matrix.h5ad"/> |
15
ca086f24422f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
630 <conditional name="method"> |
ca086f24422f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
631 <param name="method" value="pp.calculate_qc_metrics"/> |
ca086f24422f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
632 <param name="qc_vars" value="mito,negative"/> |
ca086f24422f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
633 <param name="percent_top" value="50,100,200,300"/> |
ca086f24422f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
634 </conditional> |
ca086f24422f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
635 <section name="advanced_common"> |
ca086f24422f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
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diff
changeset
|
636 <param name="show_log" value="true" /> |
ca086f24422f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
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diff
changeset
|
637 </section> |
ca086f24422f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
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diff
changeset
|
638 <output name="hidden_output"> |
ca086f24422f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
639 <assert_contents> |
ca086f24422f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
640 <has_text_matching expression="sc.pp.calculate_qc_metrics" /> |
ca086f24422f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
641 <has_text_matching expression="expr_type='counts'" /> |
ca086f24422f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
642 <has_text_matching expression="var_type='genes'" /> |
ca086f24422f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
643 <has_text_matching expression="qc_vars=\['mito', 'negative'\]" /> |
ca086f24422f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
644 <has_text_matching expression="percent_top=\[50, 100, 200, 300\]" /> |
ca086f24422f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
645 </assert_contents> |
ca086f24422f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
646 </output> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
647 <output name="anndata_out" ftype="h5ad"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
648 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
649 <has_h5_keys keys="obs/n_genes_by_counts,obs/log1p_n_genes_by_counts,obs/total_counts,obs/log1p_total_counts,obs/pct_counts_in_top_50_genes,obs/pct_counts_in_top_100_genes,obs/pct_counts_in_top_200_genes,obs/pct_counts_in_top_300_genes,obs/total_counts_mito,obs/log1p_total_counts_mito,obs/pct_counts_mito,obs/total_counts_negative,obs/log1p_total_counts_negative,obs/pct_counts_negative"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
650 <has_h5_keys keys="var/mito,var/negative,var/n_cells_by_counts,var/mean_counts,var/log1p_mean_counts,var/pct_dropout_by_counts,var/total_counts,var/log1p_total_counts"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
651 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
652 </output> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
653 </test> |
18
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
654 |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
655 <!-- test 3 --> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
656 <test expect_num_outputs="2"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
657 <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
658 <conditional name="method"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
659 <param name="method" value="pp.neighbors"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
660 </conditional> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
661 <section name="advanced_common"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
662 <param name="show_log" value="true"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
663 </section> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
664 <output name="hidden_output"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
665 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
666 <has_text_matching expression="sc.pp.neighbors"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
667 <has_text_matching expression="n_neighbors=15"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
668 <has_text_matching expression="knn=True"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
669 <has_text_matching expression="random_state=0"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
670 <has_text_matching expression="method='umap'"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
671 <has_text_matching expression="metric='euclidean'"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
672 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
673 </output> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
674 <output name="anndata_out" ftype="h5ad"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
675 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
676 <has_h5_keys keys="uns/neighbors"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
677 <has_h5_keys keys="obsp/connectivities,obsp/distances"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
678 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
679 </output> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
680 </test> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
681 |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
682 <!-- test 4 --> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
683 <test expect_num_outputs="2"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
684 <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
685 <conditional name="method"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
686 <param name="method" value="pp.neighbors"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
687 <param name="pp_neighbors_method" value="gauss"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
688 <param name="metric" value="braycurtis"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
689 </conditional> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
690 <section name="advanced_common"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
691 <param name="show_log" value="true"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
692 </section> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
693 <output name="hidden_output"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
694 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
695 <has_text_matching expression="sc.pp.neighbors"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
696 <has_text_matching expression="n_neighbors=15"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
697 <has_text_matching expression="knn=True"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
698 <has_text_matching expression="random_state=0"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
699 <has_text_matching expression="method='gauss'"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
700 <has_text_matching expression="metric='braycurtis'"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
701 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
702 </output> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
703 <output name="anndata_out" ftype="h5ad"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
704 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
705 <has_h5_keys keys="obsp/connectivities,obsp/distances"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
706 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
707 </output> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
708 </test> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
709 |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
710 <!-- test 5 --> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
711 <test expect_num_outputs="2"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
712 <param name="adata" value="krumsiek11.h5ad"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
713 <conditional name="method"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
714 <param name="method" value="tl.score_genes"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
715 <param name="gene_list" value="Gata2, Fog1"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
716 <param name="ctrl_size" value="2"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
717 <param name="n_bins" value="2"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
718 <param name="random_state" value="2"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
719 </conditional> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
720 <section name="advanced_common"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
721 <param name="show_log" value="true"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
722 </section> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
723 <output name="hidden_output"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
724 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
725 <has_text_matching expression="sc.tl.score_genes"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
726 <has_text_matching expression="gene_list=\['Gata2', 'Fog1'\]"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
727 <has_text_matching expression="ctrl_size=2"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
728 <has_text_matching expression="score_name='score'"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
729 <has_text_matching expression="n_bins=2"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
730 <has_text_matching expression="random_state=2"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
731 <has_text_matching expression="use_raw=False"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
732 <has_text_matching expression="copy=False"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
733 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
734 </output> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
735 <output name="anndata_out" ftype="h5ad"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
736 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
737 <has_h5_keys keys="obs/score"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
738 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
739 </output> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
740 </test> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
741 |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
742 <!-- test 6 --> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
743 <test expect_num_outputs="2"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
744 <param name="adata" value="krumsiek11.h5ad"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
745 <conditional name="method"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
746 <param name="method" value="tl.score_genes_cell_cycle"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
747 <conditional name='s_genes'> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
748 <param name="format" value="text"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
749 <param name="text" value="Gata2, Fog1, EgrNab"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
750 </conditional> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
751 <conditional name='g2m_genes'> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
752 <param name="format" value="text"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
753 <param name="text" value="Gata2, Fog1, EgrNab"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
754 </conditional> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
755 <param name="n_bins" value="2"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
756 <param name="random_state" value="1"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
757 </conditional> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
758 <section name="advanced_common"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
759 <param name="show_log" value="true"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
760 </section> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
761 <output name="hidden_output"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
762 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
763 <has_text_matching expression="sc.tl.score_genes_cell_cycle"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
764 <has_text_matching expression="s_genes=\['Gata2', 'Fog1', 'EgrNab'\]"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
765 <has_text_matching expression="g2m_genes=\['Gata2', 'Fog1', 'EgrNab'\]"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
766 <has_text_matching expression="n_bins=2"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
767 <has_text_matching expression="random_state=1"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
768 <has_text_matching expression="use_raw=False"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
769 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
770 </output> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
771 <output name="anndata_out" ftype="h5ad"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
772 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
773 <has_h5_keys keys="obs/S_score,obs/G2M_score,obs/phase"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
774 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
775 </output> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
776 </test> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
777 |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
778 <!-- test 7 --> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
779 <test expect_num_outputs="2"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
780 <param name="adata" value="krumsiek11.h5ad"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
781 <conditional name="method"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
782 <param name="method" value="tl.rank_genes_groups"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
783 <param name="groupby" value="cell_type"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
784 <param name="n_genes" value="100"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
785 <conditional name="tl_rank_genes_groups_method"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
786 <param name="method" value="t-test_overestim_var"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
787 </conditional> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
788 </conditional> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
789 <section name="advanced_common"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
790 <param name="show_log" value="true"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
791 </section> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
792 <output name="hidden_output"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
793 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
794 <has_text_matching expression="sc.tl.rank_genes_groups"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
795 <has_text_matching expression="groupby='cell_type'"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
796 <has_text_matching expression="use_raw=False"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
797 <has_text_matching expression="reference='rest'"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
798 <has_text_matching expression="n_genes=100"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
799 <has_text_matching expression="method='t-test_overestim_var'"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
800 <has_text_matching expression="corr_method='benjamini-hochberg'"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
801 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
802 </output> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
803 <output name="anndata_out" ftype="h5ad"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
804 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
805 <has_h5_keys keys="uns/rank_genes_groups"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
806 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
807 </output> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
808 </test> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
809 |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
810 <!-- test 8 --> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
811 <test expect_num_outputs="2"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
812 <param name="adata" value="krumsiek11.h5ad"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
813 <conditional name="method"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
814 <param name="method" value="tl.rank_genes_groups"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
815 <param name="groupby" value="cell_type"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
816 <param name="n_genes" value="100"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
817 <conditional name="tl_rank_genes_groups_method"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
818 <param name="method" value="logreg"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
819 </conditional> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
820 </conditional> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
821 <section name="advanced_common"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
822 <param name="show_log" value="true"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
823 </section> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
824 <output name="hidden_output"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
825 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
826 <has_text_matching expression="sc.tl.rank_genes_groups"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
827 <has_text_matching expression="groupby='cell_type'"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
828 <has_text_matching expression="use_raw=False"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
829 <has_text_matching expression="reference='rest'"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
830 <has_text_matching expression="n_genes=100"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
831 <has_text_matching expression="method='logreg'"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
832 <has_text_matching expression="solver='lbfgs'"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
833 <has_text_matching expression="penalty='l2'"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
834 <has_text_matching expression="fit_intercept=True"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
835 <has_text_matching expression="max_iter=100"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
836 <has_text_matching expression="multi_class='auto'"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
837 <has_text_matching expression="tol=0.0001"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
838 <has_text_matching expression="C=1.0"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
839 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
840 </output> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
841 <output name="anndata_out" ftype="h5ad"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
842 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
843 <has_h5_keys keys="uns/rank_genes_groups"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
844 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
845 </output> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
846 </test> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
847 |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
848 <!-- test 9 --> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
849 <test expect_num_outputs="2"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
850 <param name="adata" value="krumsiek11.h5ad"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
851 <conditional name="method"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
852 <param name="method" value="tl.rank_genes_groups"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
853 <param name="groupby" value="cell_type"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
854 <param name="n_genes" value="100"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
855 <conditional name="tl_rank_genes_groups_method"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
856 <param name="method" value="logreg"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
857 <conditional name="solver"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
858 <param name="solver" value="liblinear"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
859 <conditional name="penalty"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
860 <param name="penalty" value="l2"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
861 <param name="random_state" value="1"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
862 </conditional> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
863 </conditional> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
864 </conditional> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
865 </conditional> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
866 <section name="advanced_common"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
867 <param name="show_log" value="true"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
868 </section> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
869 <output name="hidden_output"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
870 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
871 <has_text_matching expression="sc.tl.rank_genes_groups"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
872 <has_text_matching expression="groupby='cell_type'"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
873 <has_text_matching expression="use_raw=False"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
874 <has_text_matching expression="reference='rest'"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
875 <has_text_matching expression="n_genes=100"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
876 <has_text_matching expression="method='logreg'"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
877 <has_text_matching expression="solver='liblinear'"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
878 <has_text_matching expression="penalty='l2'"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
879 <has_text_matching expression="dual=False"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
880 <has_text_matching expression="fit_intercept=True"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
881 <has_text_matching expression="intercept_scaling=1.0"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
882 <has_text_matching expression="tol=0.0001"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
883 <has_text_matching expression="C=1.0"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
884 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
885 </output> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
886 <output name="anndata_out" ftype="h5ad"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
887 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
888 <has_h5_keys keys="uns/rank_genes_groups"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
889 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
890 </output> |
18
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
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diff
changeset
|
891 </test> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
892 |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
893 <!-- test 10 --> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
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|
894 <test expect_num_outputs="2"> |
18
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
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diff
changeset
|
895 <param name="adata" value="krumsiek11.h5ad"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
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diff
changeset
|
896 <conditional name="method"> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
897 <param name="method" value="tl.rank_genes_groups"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
898 <param name="groupby" value="cell_type"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
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diff
changeset
|
899 <param name="groups" value="Ery"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
900 <conditional name="ref"> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
901 <param name="rest" value="group_id"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
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diff
changeset
|
902 <param name="reference" value="Mk"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
903 </conditional> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
904 <param name="n_genes" value="100"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
905 <conditional name="tl_rank_genes_groups_method"> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
906 <param name="method" value="logreg"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
907 <conditional name="solver"> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
908 <param name="solver" value="liblinear"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
909 <conditional name="penalty"> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
910 <param name="penalty" value="l2"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
911 <param name="random_state" value="1"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
912 </conditional> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
913 </conditional> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
914 </conditional> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
915 </conditional> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
916 <section name="advanced_common"> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
917 <param name="show_log" value="true"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
918 </section> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
919 <output name="hidden_output"> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
920 <assert_contents> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
921 <has_text_matching expression="sc.tl.rank_genes_groups"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
922 <has_text_matching expression="groupby='cell_type'"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
923 <has_text_matching expression="use_raw=False"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
924 <has_text_matching expression="n_genes=100"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
925 <has_text_matching expression="method='logreg'"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
926 <has_text_matching expression="solver='liblinear'"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
927 <has_text_matching expression="penalty='l2'"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
928 <has_text_matching expression="dual=False"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
929 <has_text_matching expression="fit_intercept=True"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
930 <has_text_matching expression="intercept_scaling=1.0"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
931 <has_text_matching expression="tol=0.0001"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
932 <has_text_matching expression="C=1.0"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
933 <has_text_matching expression="groups=\['Ery'\]"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
934 <has_text_matching expression="reference='Mk'"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
935 </assert_contents> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
936 </output> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
937 <output name="anndata_out" ftype="h5ad"> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
938 <assert_contents> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
939 <has_h5_keys keys="uns/rank_genes_groups"/> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
940 </assert_contents> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
941 </output> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
942 </test> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
943 |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
944 <!-- test 11 --> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
945 <test expect_num_outputs="2"> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
946 <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_reduced.h5ad"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
947 <conditional name="method"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
948 <param name="method" value="tl.marker_gene_overlap"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
949 <repeat name="reference_markers"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
950 <param name="key" value="CD4 T cells"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
951 <param name="values" value="IL7R"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
952 </repeat> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
953 <repeat name="reference_markers"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
954 <param name="key" value="CD14+ Monocytes"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
955 <param name="values" value="CD14,LYZ"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
956 </repeat> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
957 <repeat name="reference_markers"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
958 <param name="key" value="B cells"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
959 <param name="values" value="MS4A1"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
960 </repeat> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
961 </conditional> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
962 <section name="advanced_common"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
963 <param name="show_log" value="true"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
964 </section> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
965 <assert_stdout> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
966 <has_text_matching expression="marker_gene_overlap"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
967 </assert_stdout> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
968 <output name="hidden_output"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
969 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
970 <has_text_matching expression="sc.tl.marker_gene_overlap"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
971 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
972 </output> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
973 <output name="anndata_out" ftype="h5ad"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
974 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
975 <has_h5_keys keys="uns/rank_genes_groups"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
976 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
977 </output> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
978 </test> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
979 |
18
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
980 <!-- test 12 --> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
981 <test expect_num_outputs="2"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
982 <param name="adata" value="krumsiek11.h5ad"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
983 <conditional name="method"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
984 <param name="method" value="pp.log1p"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
985 </conditional> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
986 <section name="advanced_common"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
987 <param name="show_log" value="true"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
988 </section> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
989 <output name="hidden_output"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
990 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
991 <has_text_matching expression="sc.pp.log1p"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
992 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
993 </output> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
994 <output name="anndata_out" ftype="h5ad"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
995 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
996 <has_h5_keys keys="uns/log1p"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
997 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
998 </output> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
999 </test> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
1000 |
18
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
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diff
changeset
|
1001 <!-- test 13 --> |
17
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
1002 <test expect_num_outputs="2"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
1003 <param name="adata" value="krumsiek11.h5ad"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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changeset
|
1004 <conditional name="method"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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changeset
|
1005 <param name="method" value="pp.scale"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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changeset
|
1006 </conditional> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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changeset
|
1007 <section name="advanced_common"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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changeset
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1008 <param name="show_log" value="true"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
1009 </section> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
1010 <output name="hidden_output"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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changeset
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1011 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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changeset
|
1012 <has_text_matching expression="sc.pp.scale"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
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1013 <has_text_matching expression="zero_center=True"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
1014 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
1015 </output> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
changeset
|
1016 <output name="anndata_out" ftype="h5ad"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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changeset
|
1017 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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changeset
|
1018 <has_h5_keys keys="var/mean,var/std"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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changeset
|
1019 </assert_contents> |
18
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
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diff
changeset
|
1020 </output> |
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
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diff
changeset
|
1021 </test> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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diff
changeset
|
1022 |
18
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
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17
diff
changeset
|
1023 <!-- test 14 --> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1024 <test expect_num_outputs="2"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1025 <param name="adata" value="krumsiek11.h5ad"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1026 <conditional name="method"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1027 <param name="method" value="pp.scale"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1028 <param name="max_value" value="10"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1029 </conditional> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1030 <section name="advanced_common"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1031 <param name="show_log" value="true"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1032 </section> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1033 <output name="hidden_output"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1034 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1035 <has_text_matching expression="sc.pp.scale"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1036 <has_text_matching expression="zero_center=True"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1037 <has_text_matching expression="max_value=10.0"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1038 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1039 </output> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1040 <output name="anndata_out" ftype="h5ad"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1041 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1042 <has_h5_keys keys="var/mean,var/std"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1043 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1044 </output> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1045 </test> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1046 |
18
d1cd8c147809
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents:
17
diff
changeset
|
1047 <!-- test 15 --> |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1048 <test expect_num_outputs="2"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1049 <param name="adata" value="random-randint.h5ad"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1050 <conditional name="method"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1051 <param name="method" value="pp.sqrt"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1052 </conditional> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1053 <section name="advanced_common"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1054 <param name="show_log" value="true"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1055 </section> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1056 <output name="hidden_output"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1057 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1058 <has_text_matching expression="sc.pp.sqrt"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1059 <has_text_matching expression="stats before sqrt: min= 0.0 max= 999.0 mean= 499.83777"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1060 <has_text_matching expression="stats after sqrt: min= 0.0 max= 31.606962 mean= 21.079018"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1061 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1062 </output> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1063 <output name="anndata_out" ftype="h5ad"> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1064 <assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1065 <has_h5_keys keys="obs/index"/> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1066 </assert_contents> |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
15
diff
changeset
|
1067 </output> |
15
ca086f24422f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents:
14
diff
changeset
|
1068 </test> |
20
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1069 |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1070 <!-- test 16 --> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1071 <test expect_num_outputs="3"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1072 <param name="adata" value="krumsiek11.h5ad"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1073 <conditional name="method"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1074 <param name="method" value="tl.rank_genes_groups"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1075 <conditional name="get_df"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1076 <param name="get_df_select" value="True"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1077 </conditional> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1078 <param name="groupby" value="cell_type"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1079 <param name="n_genes" value="100"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1080 <conditional name="tl_rank_genes_groups_method"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1081 <param name="method" value="t-test_overestim_var"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1082 </conditional> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1083 </conditional> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1084 <section name="advanced_common"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1085 <param name="show_log" value="true"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1086 </section> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1087 <output name="hidden_output"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1088 <assert_contents> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1089 <has_text_matching expression="sc.tl.rank_genes_groups"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1090 <has_text_matching expression="groupby='cell_type'"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1091 <has_text_matching expression="use_raw=False"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1092 <has_text_matching expression="reference='rest'"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1093 <has_text_matching expression="n_genes=100"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1094 <has_text_matching expression="method='t-test_overestim_var'"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1095 <has_text_matching expression="corr_method='benjamini-hochberg'"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1096 <has_text_matching expression="sc.get.rank_genes_groups_df"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1097 </assert_contents> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1098 </output> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1099 <output name="anndata_out" ftype="h5ad"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1100 <assert_contents> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1101 <has_h5_keys keys="uns/rank_genes_groups"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1102 </assert_contents> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1103 </output> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1104 <output name="ranked_gene" ftype="tabular"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
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diff
changeset
|
1105 <assert_contents> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1106 <has_line_matching expression="group\tnames\tscores\tlogfoldchanges\tpvals\tpvals_adj"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
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|
1107 <has_line_matching expression="Ery\tEKLF\t39.086777\t4.8413053\t1.7995717323073084e-66\t1.979528905538039e-65"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1108 </assert_contents> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1109 </output> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1110 </test> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1111 |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1112 <!-- test 17 --> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1113 <test expect_num_outputs="3"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1114 <param name="adata" value="krumsiek11.h5ad"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1115 <conditional name="method"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1116 <param name="method" value="tl.rank_genes_groups"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1117 <conditional name="get_df"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1118 <param name="get_df_select" value="True"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1119 </conditional> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1120 <param name="groupby" value="cell_type"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1121 <param name="groups" value="Ery"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1122 <conditional name="ref"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1123 <param name="rest" value="group_id"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1124 <param name="reference" value="Mk"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1125 </conditional> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1126 <param name="n_genes" value="100"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1127 <conditional name="tl_rank_genes_groups_method"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1128 <param name="method" value="logreg"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1129 <conditional name="solver"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1130 <param name="solver" value="liblinear"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1131 <conditional name="penalty"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1132 <param name="penalty" value="l2"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1133 <param name="random_state" value="1"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1134 </conditional> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1135 </conditional> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1136 </conditional> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1137 </conditional> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1138 <section name="advanced_common"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1139 <param name="show_log" value="true"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1140 </section> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1141 <output name="hidden_output"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1142 <assert_contents> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1143 <has_text_matching expression="sc.tl.rank_genes_groups"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1144 <has_text_matching expression="groupby='cell_type'"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1145 <has_text_matching expression="use_raw=False"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1146 <has_text_matching expression="n_genes=100"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1147 <has_text_matching expression="method='logreg'"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1148 <has_text_matching expression="solver='liblinear'"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1149 <has_text_matching expression="penalty='l2'"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1150 <has_text_matching expression="dual=False"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1151 <has_text_matching expression="fit_intercept=True"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1152 <has_text_matching expression="intercept_scaling=1.0"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1153 <has_text_matching expression="tol=0.0001"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1154 <has_text_matching expression="C=1.0"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1155 <has_text_matching expression="groups=\['Ery'\]"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1156 <has_text_matching expression="reference='Mk'"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1157 <has_text_matching expression="sc.get.rank_genes_groups_df"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1158 </assert_contents> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1159 </output> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1160 <output name="anndata_out" ftype="h5ad"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1161 <assert_contents> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1162 <has_h5_keys keys="uns/rank_genes_groups"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1163 </assert_contents> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1164 </output> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1165 <output name="ranked_gene" ftype="tabular"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1166 <assert_contents> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1167 <has_text_matching expression="names\tscores"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1168 <has_text_matching expression="Fli1\t3.5328505"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1169 </assert_contents> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1170 </output> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1171 </test> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1172 |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1173 <!-- test 18 --> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1174 <test expect_num_outputs="3"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1175 <param name="adata" value="krumsiek11.h5ad"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1176 <conditional name="method"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1177 <param name="method" value="tl.rank_genes_groups"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1178 <conditional name="get_df"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1179 <param name="get_df_select" value="True"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1180 <param name="pval_cutoff" value="0.05"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1181 <param name="log2fc_min" value="1"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
changeset
|
1182 <param name="log2fc_max" value="3"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
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|
1183 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1184 <param name="groupby" value="cell_type"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1185 <param name="n_genes" value="100"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1186 <conditional name="tl_rank_genes_groups_method"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1187 <param name="method" value="t-test_overestim_var"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1188 </conditional> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1189 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1190 <section name="advanced_common"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1191 <param name="show_log" value="true"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1192 </section> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1193 <output name="hidden_output"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1194 <assert_contents> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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parents:
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|
1195 <has_text_matching expression="sc.tl.rank_genes_groups"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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18
diff
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|
1196 <has_text_matching expression="groupby='cell_type'"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1197 <has_text_matching expression="use_raw=False"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1198 <has_text_matching expression="reference='rest'"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1199 <has_text_matching expression="n_genes=100"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1200 <has_text_matching expression="method='t-test_overestim_var'"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1201 <has_text_matching expression="corr_method='benjamini-hochberg'"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1202 <has_text_matching expression="sc.get.rank_genes_groups_df"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1203 <has_text_matching expression="pval_cutoff=0.05"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
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18
diff
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|
1204 <has_text_matching expression="log2fc_min=1"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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diff
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|
1205 <has_text_matching expression="log2fc_max=3"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1206 </assert_contents> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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diff
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|
1207 </output> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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diff
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|
1208 <output name="anndata_out" ftype="h5ad"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1209 <assert_contents> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1210 <has_h5_keys keys="uns/rank_genes_groups"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1211 </assert_contents> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1212 </output> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1213 <output name="ranked_gene" ftype="tabular"> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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|
1214 <assert_contents> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
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|
1215 <has_line_matching expression="group\tnames\tscores\tlogfoldchanges\tpvals\tpvals_adj"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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diff
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|
1216 <has_line_matching expression="Ery\tFog1\t21.071571\t2.8023682\t5.701001345880348e-35\t3.135550740234191e-34"/> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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18
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|
1217 </assert_contents> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
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18
diff
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|
1218 </output> |
d86cb2ce311b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
iuc
parents:
18
diff
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|
1219 </test> |
0
5d2e17328afe
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iuc
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diff
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|
1220 </tests> |
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
1221 <help><![CDATA[ |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1222 Calculate quality control metrics., using `pp.calculate_qc_metrics` |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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|
1223 =================================================================== |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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0
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|
1224 |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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15
diff
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|
1225 Calculates a number of qc metrics for an AnnData object, largely based on calculateQCMetrics from scater. |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1226 Currently is most efficient on a sparse CSR or dense matrix. |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1227 |
3
cc0deb593fc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents:
2
diff
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|
1228 It updates the observation level metrics with |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1229 |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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|
1230 - total_{var_type}_by_{expr_type} (e.g. "total_genes_by_counts", number of genes with positive counts in a cell) |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1231 - total_{expr_type} (e.g. "total_counts", total number of counts for a cell) |
3
cc0deb593fc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents:
2
diff
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|
1232 - pct_{expr_type}_in_top_{n}_{var_type} - for n in percent_top (e.g. "pct_counts_in_top_50_genes", cumulative percentage of counts for 50 most expressed genes in a cell) |
cc0deb593fc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents:
2
diff
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|
1233 - total_{expr_type}_{qc_var} - for qc_var in qc_vars (e.g. "total_counts_mito", total number of counts for variabes in qc_vars) |
cc0deb593fc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents:
2
diff
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|
1234 - pct_{expr_type}_{qc_var} - for qc_var in qc_vars (e.g. "pct_counts_mito", proportion of total counts for a cell which are mitochondrial) |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1235 |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1236 And also the variable level metrics: |
0
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
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|
1237 |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1238 - total_{expr_type} (e.g. "total_counts", sum of counts for a gene) |
3
cc0deb593fc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents:
2
diff
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|
1239 - mean_{expr_type} (e.g. "mean counts", mean expression over all cells) |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1240 - n_cells_by_{expr_type} (e.g. "n_cells_by_counts", number of cells this expression is measured in) |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1241 - pct_dropout_by_{expr_type} (e.g. "pct_dropout_by_counts", percentage of cells this feature does not appear in) |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1242 |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1243 More details on the `scanpy documentation |
14
f54f0f0598ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents:
12
diff
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|
1244 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.calculate_qc_metrics.html>`__ |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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|
1245 |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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|
1246 Compute a neighborhood graph of observations, using `pp.neighbors` |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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|
1247 ================================================================== |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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|
1248 |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1249 The neighbor search efficiency of this heavily relies on UMAP (McInnes et al, 2018), |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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|
1250 which also provides a method for estimating connectivities of data points - |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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|
1251 the connectivity of the manifold (`method=='umap'`). If `method=='diffmap'`, |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1252 connectivities are computed according to Coifman et al (2005), in the adaption of |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1253 Haghverdi et al (2016). |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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|
1254 |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1255 The returned AnnData object contains: |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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|
1256 |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1257 - Weighted adjacency matrix of the neighborhood graph of data points (connectivities). Weights should be interpreted as connectivities. |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1258 - Distances for each pair of neighbors (distances) |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1259 |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1260 This data are stored in the unstructured annotation (uns) and can be accessed using the inspect tool for AnnData objects |
0
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
1261 |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1262 More details on the `scanpy documentation |
14
f54f0f0598ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents:
12
diff
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|
1263 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.neighbors.html>`__ |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1264 |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1265 Score a set of genes, using `tl.score_genes` |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1266 ============================================ |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1267 |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1268 The score is the average expression of a set of genes subtracted with the |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1269 average expression of a reference set of genes. The reference set is |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1270 randomly sampled from the `gene_pool` for each binned expression value. |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1271 |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1272 This reproduces the approach in Seurat (Satija et al, 2015) and has been implemented |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1273 for Scanpy by Davide Cittaro. |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1274 |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1275 More details on the `scanpy documentation |
14
f54f0f0598ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents:
12
diff
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|
1276 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.score_genes.html>`__ |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1277 |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1278 Score cell cycle genes, using `tl.score_genes_cell_cycle` |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1279 ========================================================= |
0
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
1280 |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1281 Given two lists of genes associated to S phase and G2M phase, calculates |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1282 scores and assigns a cell cycle phase (G1, S or G2M). See |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1283 `score_genes` for more explanation. |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1284 |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
1285 More details on the `scanpy documentation |
14
f54f0f0598ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents:
12
diff
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|
1286 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.score_genes_cell_cycle.html>`__ |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1287 |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1288 Rank genes for characterizing groups, using `tl.rank_genes_groups` |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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diff
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|
1289 ================================================================== |
0
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
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|
1290 |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1291 The returned AnnData object contains: |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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|
1292 |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1293 - Gene names, ordered according to scores |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1294 - Z-score underlying the computation of a p-value for each gene for each group, prdered according to scores |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1295 - Log2 fold change for each gene for each group, ordered according to scores. It is only provided if method is ‘t-test’ like. This is an approximation calculated from mean-log values. |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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|
1296 - P-values |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1297 - Ajusted p-values |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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0
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|
1298 |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1299 This data are stored in the unstructured annotation (uns) and can be accessed using the inspect tool for AnnData objects |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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|
1300 |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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|
1301 More details on the `scanpy documentation |
14
f54f0f0598ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
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|
1302 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.rank_genes_groups.html>`__ |
0
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
changeset
|
1303 |
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff
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|
1304 |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
1305 Calculate an overlap score between data-deriven marker genes and provided markers (`tl.marker_gene_overlap`) |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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|
1306 ============================================================================================================ |
0
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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|
1307 |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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|
1308 Marker gene overlap scores can be quoted as overlap counts, overlap coefficients, or jaccard indices. The method returns a pandas dataframe which can be used to annotate clusters based on marker gene overlaps. |
0
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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|
1309 |
17
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents:
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diff
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|
1310 More details on the `scanpy documentation |
18262103fa61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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|
1311 <https://scanpy.readthedocs.io/en/stable/generated/scanpy.tl.marker_gene_overlap.html>`__ |
0
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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|
1312 |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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|
1313 Logarithmize the data matrix (`pp.log1p`) |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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|
1314 ========================================= |
0
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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|
1315 |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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|
1316 More details on the `scanpy documentation |
14
f54f0f0598ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
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|
1317 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.log1p.html>`__ |
0
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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parents:
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|
1318 |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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|
1319 Scale data to unit variance and zero mean (`pp.scale`) |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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|
1320 ====================================================== |
0
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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|
1321 |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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0
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|
1322 More details on the `scanpy documentation |
14
f54f0f0598ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
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|
1323 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.scale.html>`__ |
0
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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|
1324 |
1
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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|
1325 Computes the square root the data matrix (`pp.sqrt`) |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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|
1326 ==================================================== |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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|
1327 |
a755eaa1cc32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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|
1328 `X = sqrt(X)` |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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|
1329 ]]></help> |
5d2e17328afe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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|
1330 <expand macro="citations"/> |
6
5e9171dc8244
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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|
1331 </tool> |