Mercurial > repos > iuc > scanpy_inspect

annotate inspect.xml @ 18:d1cd8c147809 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
author iuc
date Thu, 19 Sep 2024 06:43:47 +0000
parents 18262103fa61
children
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d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
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1 <tool id="scanpy_inspect" name="Scanpy Inspect and manipulate" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
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2 <macros>
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3 <import>macros.xml</import>
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4 <xml name="params_score_genes">
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5 <param argument="n_bins" type="integer" value="25" label="Number of expression level bins for sampling"/>
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6 <param argument="random_state" type="integer" value="0" label="Random seed for sampling"/>
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7 <expand macro="param_use_raw"/>
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8 </xml>
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9 <token name="@CMD_PARAMS_SCORE_GENES@"><![CDATA[
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10 n_bins=$method.n_bins,
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11 random_state=$method.random_state,
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12 use_raw=$method.use_raw,
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13 copy=False
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14 ]]>
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15 </token>
1
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16 <xml name="corr_method">
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17 <param argument="corr_method" type="select" label="P-value correction method">
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18 <option value="benjamini-hochberg" selected="true">Benjamini-Hochberg</option>
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19 <option value="bonferroni">Bonferroni</option>
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20 </param>
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21 </xml>
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22 <xml name="fit_intercept">
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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?"/>
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24 </xml>
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25 <xml name="max_iter">
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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"/>
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27 </xml>
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28 <xml name="multi_class">
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29 <param argument="multi_class" type="select" label="Multi class">
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30 <option value="auto" selected="true">auto: selects ‘ovr’ if the data is binary and otherwise selects ‘multinomial’</option>
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31 <option value="ovr">ovr: a binary problem is fit for each label</option>
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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>
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33 </param>
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34 </xml>
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35 <xml name="penalty">
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36 <param argument="penalty" type="select" label="Norm used in the penalization">
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37 <option value="l2" selected="true">l2</option>
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38 <option value="l1">l1</option>
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39 <yield/>
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40 </param>
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41 </xml>
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42 <xml name="random_state">
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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"/>
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44 </xml>
0
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45 </macros>
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46 <expand macro="bio_tools"/>
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47 <expand macro="requirements">
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48 <requirement type="package" version="1.5.1">scikit-learn</requirement>
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49 </expand>
0
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50 <expand macro="version_command"/>
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51 <command detect_errors="exit_code"><![CDATA[
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52 @CMD@
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53 ]]></command>
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54 <configfiles>
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55 <configfile name="script_file"><![CDATA[
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56 @CMD_IMPORTS@
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57 @CMD_READ_INPUTS@
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58
17
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59 #if str($method.method) == 'pp.calculate_qc_metrics':
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60 sc.pp.calculate_qc_metrics(
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61 adata=adata,
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62 expr_type='$method.expr_type',
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63 var_type='$method.var_type',
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64 #if str($method.qc_vars) != '':
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65 #set $qc_vars = [str(x.strip()) for x in str($method.qc_vars).split(',')]
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66 qc_vars=$qc_vars,
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67 #end if
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68 #if str($method.percent_top) != '':
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69 #set $percent_top = [int(x.strip()) for x in str($method.percent_top).split(',')]
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70 percent_top=$percent_top,
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71 #end if
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72 #if str($method.layer) != '':
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73 layer='$method.layer',
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74 #end if
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75 use_raw=$method.use_raw,
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76 log1p=$method.log1p,
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77 inplace=True)
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78
17
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79 #else if str($method.method) == 'pp.neighbors':
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80 sc.pp.neighbors(
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81 adata=adata,
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82 n_neighbors=$method.n_neighbors,
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83 #if str($method.n_pcs) != '':
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84 n_pcs=$method.n_pcs,
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85 #end if
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
86 #if str($method.use_rep) != '':
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
87 use_rep='$method.use_rep',
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
88 #end if
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
89 knn=$method.knn,
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
90 method='$method.pp_neighbors_method',
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
91 metric='$method.metric',
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iuc
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diff changeset
92 random_state=$method.random_state,
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
93 #if str($method.key_added) != '':
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
94 key_added='$method.key_added',
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
95 #end if
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
96 copy=False)
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
97
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
98 #else if str($method.method) == 'tl.score_genes':
1
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iuc
parents: 0
diff changeset
99 sc.tl.score_genes(
0
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iuc
parents:
diff changeset
100 adata=adata,
1
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iuc
parents: 0
diff changeset
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"
iuc
parents: 0
diff changeset
102 gene_list=$gene_list,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
103 ctrl_size=$method.ctrl_size,
17
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iuc
parents: 15
diff changeset
104 #if str($method.gene_pool) != '':
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
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"
iuc
parents: 0
diff changeset
106 gene_pool=$gene_pool,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
107 #end if
17
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iuc
parents: 15
diff changeset
108 score_name='$method.score_name',
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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diff changeset
109 @CMD_PARAMS_SCORE_GENES@)
1
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parents: 0
diff changeset
110
17
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iuc
parents: 15
diff changeset
111 #else if str($method.method) == 'tl.score_genes_cell_cycle':
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
112 #if str($method.s_genes.format) == 'file':
1
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parents: 0
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113 with open('$method.s_genes.file', 'r') as s_genes_f:
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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114 s_genes = [str(x.strip()) for x in s_genes_f.readlines()]
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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115 print(s_genes)
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parents: 0
diff changeset
116 #end if
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117
17
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iuc
parents: 15
diff changeset
118 #if str($method.g2m_genes.format) == 'file':
1
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iuc
parents: 0
diff changeset
119 with open('$method.g2m_genes.file', 'r') as g2m_genes_f:
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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120 g2m_genes = [str(x.strip()) for x in g2m_genes_f.readlines()]
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
121 print(g2m_genes)
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
122 #end if
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
123
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
124 sc.tl.score_genes_cell_cycle(
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
125 adata=adata,
17
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iuc
parents: 15
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126 #if str($method.s_genes.format) == 'text':
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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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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128 s_genes=$s_genes,
17
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iuc
parents: 15
diff changeset
129 #else if str($method.s_genes.format) == 'file':
1
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130 s_genes=s_genes,
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iuc
parents: 0
diff changeset
131 #end if
17
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iuc
parents: 15
diff changeset
132 #if str($method.g2m_genes.format) == 'text':
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iuc
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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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134 g2m_genes=$g2m_genes,
17
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iuc
parents: 15
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135 #else if str($method.g2m_genes.format) == 'file':
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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136 g2m_genes=g2m_genes,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
137 #end if
17
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iuc
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138 @CMD_PARAMS_SCORE_GENES@)
1
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139
17
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iuc
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140 #else if str($method.method) == 'tl.rank_genes_groups':
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
141 sc.tl.rank_genes_groups(
0
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iuc
parents:
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142 adata=adata,
17
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iuc
parents: 15
diff changeset
143 #if str($method.groupby) != '':
1
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parents: 0
diff changeset
144 groupby='$method.groupby',
17
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iuc
parents: 15
diff changeset
145 #end if
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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diff changeset
146 use_raw=$method.use_raw,
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
147 #if str($method.groups) != '':
1
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iuc
parents: 0
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148 #set $group=[x.strip() for x in str($method.groups).split(',')]
18
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
149 groups=$group,
1
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parents: 0
diff changeset
150 #end if
17
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iuc
parents: 15
diff changeset
151 #if str($method.layer) != '':
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iuc
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diff changeset
152 layer='$method.layer',
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iuc
parents: 15
diff changeset
153 #end if
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
154 #if str($method.ref.rest) == 'rest':
1
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parents: 0
diff changeset
155 reference='$method.ref.rest',
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parents: 0
diff changeset
156 #else
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parents: 0
diff changeset
157 reference='$method.ref.reference',
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
158 #end if
17
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iuc
parents: 15
diff changeset
159 #if str($method.n_genes) != '':
1
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parents: 0
diff changeset
160 n_genes=$method.n_genes,
17
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iuc
parents: 15
diff changeset
161 #end if
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
162 method='$method.tl_rank_genes_groups_method.method',
17
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iuc
parents: 15
diff changeset
163 #if str($method.tl_rank_genes_groups_method.method) != 'logreg':
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
164 corr_method='$method.tl_rank_genes_groups_method.corr_method',
17
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iuc
parents: 15
diff changeset
165 #end if
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
166 #if str($method.tl_rank_genes_groups_method.method) == 'wilcoxon':
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iuc
parents: 15
diff changeset
167 tie_correct=$method.tl_rank_genes_groups_method.tie_correct,
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
168 #end if
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
169 #if str($method.tl_rank_genes_groups_method.method) == 'logreg':
1
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iuc
parents: 0
diff changeset
170 solver='$method.tl_rank_genes_groups_method.solver.solver',
17
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iuc
parents: 15
diff changeset
171 #if str($method.tl_rank_genes_groups_method.solver.solver) == 'lbfgs':
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172 penalty='$method.tl_rank_genes_groups_method.solver.penalty',
1
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173 fit_intercept=$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',
17
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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',
1
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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='$method.tl_rank_genes_groups_method.solver.multi_class',
17
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181 #else if str($method.tl_rank_genes_groups_method.solver.solver) == 'liblinear':
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182 #if str($method.tl_rank_genes_groups_method.solver.penalty.penalty) == 'l1':
1
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183 penalty='l1',
17
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184 #else:
1
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185 penalty='l2',
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186 dual=$method.tl_rank_genes_groups_method.solver.penalty.dual,
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187 #end if
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188 fit_intercept=$method.tl_rank_genes_groups_method.solver.intercept_scaling.fit_intercept,
17
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189 #if str($method.tl_rank_genes_groups_method.solver.intercept_scaling.fit_intercept) == 'True':
1
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190 intercept_scaling=$method.tl_rank_genes_groups_method.solver.intercept_scaling.intercept_scaling,
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191 #end if
17
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192 #if str($method.tl_rank_genes_groups_method.solver.random_state) != '':
1
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193 random_state=$method.tl_rank_genes_groups_method.solver.random_state,
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194 #end if
17
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195 #else if str($method.tl_rank_genes_groups_method.solver.solver) == 'sag':
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196 penalty='$method.tl_rank_genes_groups_method.solver.penalty.penalty',
1
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197 fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept,
17
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198 #if str($method.tl_rank_genes_groups_method.solver.random_state) != '':
1
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199 random_state=$method.tl_rank_genes_groups_method.solver.random_state,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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200 #end if
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201 max_iter=$method.tl_rank_genes_groups_method.solver.max_iter,
17
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202 multi_class=$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':
1
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205 penalty='l1',
17
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206 #else if str($method.tl_rank_genes_groups_method.solver.penalty.penalty) == 'l2':
1
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207 penalty='l2',
17
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208 #else if str($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',
1
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212 #end if
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213 fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept,
17
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214 multi_class=$method.tl_rank_genes_groups_method.solver.multi_class,
1
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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
17
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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)
1
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223
17
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224 #else if str($method.method) == "tl.marker_gene_overlap":
1
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225 reference_markers = {}
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226 #for $i, $s in enumerate($method.reference_markers)
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227 #set $list=[x.strip() for x in str($s.values).split(',')]
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228 reference_markers['$s.key'] = $list
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229 #end for
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230
17
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231 # Temporary fix for the issue with "inplace=True" for Pandas dataframes.
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232 # see here: https://github.com/scverse/scanpy/blob/b6193502e11b84fc1b4a011ee9cf08a19da22ebf/src/scanpy/tools/_marker_gene_overlap.py#L167
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233 marker_overlap_result = sc.tl.marker_gene_overlap(
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234 adata,
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235 reference_markers,
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236 #if str($method.key) != '':
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237 key='$method.key',
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238 #end if
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239 method='$method.overlap.method',
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240 #if str($method.overlap.method) == 'overlap_count' and str($method.overlap.normalize) != 'None':
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241 normalize='$method.overlap.normalize',
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242 #end if
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243 #if str($method.top_n_markers) != '':
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244 top_n_markers=$method.top_n_markers,
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245 #end if
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246 #if str($method.adj_pval_threshold) != '':
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247 adj_pval_threshold=$method.adj_pval_threshold,
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248 #end if
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249 #if $method.key_added:
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250 key_added='$method.key_added',
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251 #end if
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252 inplace=False)
1
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253
17
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254 adata.uns['marker_gene_overlap'] = marker_overlap_result
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255
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256 #else if str($method.method) == "pp.log1p":
1
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257 sc.pp.log1p(
8
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258 adata,
17
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259 #if str($method.base) != '':
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260 base=$method.base,
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261 #end if
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262 #if str($method.layer) != '':
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263 layer='$method.layer',
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264 #end if
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265 #if str($method.obsm) != '':
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266 obsm='$method.obsm',
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267 #end if
0
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268 copy=False)
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269
17
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270 #else if str($method.method) == "pp.scale":
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271 sc.pp.scale(
8
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272 adata,
1
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273 zero_center=$method.zero_center,
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274 #if str($method.max_value) != '':
1
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275 max_value=$method.max_value,
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276 #end if
17
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277 #if str($method.layer) != '':
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278 layer='$method.layer',
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279 #end if
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280 #if str($method.obsm) != '':
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281 obsm='$method.obsm',
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282 #end if
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283 #if str($method.mask_obs) != '':
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284 mask_obs='$method.mask_obs',
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285 #end if
1
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286 copy=False)
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287
17
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288 #else if str($method.method) == "pp.sqrt":
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289
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290 print("stats before sqrt:", "min=", adata.X.min(), "max=", adata.X.max(), "mean=", adata.X.mean())
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291
1
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292 sc.pp.sqrt(
8
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293 adata,
1
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294 copy=False)
0
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295 #end if
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296
17
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297 print("stats after sqrt:", "min=", adata.X.min(), "max=", adata.X.max(), "mean=", adata.X.mean())
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298
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299 @CMD_ANNDATA_WRITE_OUTPUTS@
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300 ]]>
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301 </configfile>
0
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302 </configfiles>
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303 <inputs>
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304 <expand macro="inputs_anndata"/>
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305 <conditional name="method">
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306 <param argument="method" type="select" label="Method used for inspecting">
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307 <option value="pp.calculate_qc_metrics">Calculate quality control metrics, using 'pp.calculate_qc_metrics'</option>
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308 <option value="pp.neighbors">Compute a neighborhood graph of observations, using 'pp.neighbors'</option>
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309 <option value="tl.score_genes">Score a set of genes, using 'tl.score_genes'</option>
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310 <option value="tl.score_genes_cell_cycle">Score cell cycle genes, using 'tl.score_genes_cell_cycle'</option>
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311 <option value="tl.rank_genes_groups">Rank genes for characterizing groups, using 'tl.rank_genes_groups'</option>
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312 <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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313 <option value="pp.log1p">Logarithmize the data matrix, using 'pp.log1p'</option>
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314 <option value="pp.scale">Scale data to unit variance and zero mean, using 'pp.scale'</option>
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315 <option value="pp.sqrt">Square root the data matrix, using 'pp.sqrt'</option>
0
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316 </param>
1
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317 <when value="pp.calculate_qc_metrics">
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318 <param argument="expr_type" type="text" value="counts" label="Name of kind of values in X">
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319 <expand macro="sanitize_query"/>
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320 </param>
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321 <param argument="var_type" type="text" value="genes" label="The kind of thing the variables are">
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322 <expand macro="sanitize_query"/>
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323 </param>
17
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324 <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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325 <expand macro="sanitize_query"/>
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326 </param>
17
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327 <param argument="percent_top" type="text" value="" optional="true" label="Proportions of top genes to cover"
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328 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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329 <expand macro="sanitize_vectors"/>
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330 </param>
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331 <expand macro="param_layer"/>
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332 <expand macro="param_use_raw"/>
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333 <param argument="log1p" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Compute log1p transformed annotations"/>
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334 </when>
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335 <when value="pp.neighbors">
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336 <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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337 <param argument="n_pcs" type="integer" min="0" value="" optional="true" label="Number of PCs to use"/>
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338 <expand macro="param_use_rep"/>
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339 <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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340 <param name="pp_neighbors_method" argument="method" type="select" label="Method for computing connectivities">
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341 <option value="umap" selected="true">umap (McInnes et al, 2018)</option>
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342 <option value="gauss">gauss: Gauss kernel following (Coifman et al 2005) with adaptive width (Haghverdi et al 2016)</option>
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343 </param>
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344 <param argument="metric" type="select" label="Distance metric">
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345 <expand macro="distance_metric_options"/>
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346 </param>
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347 <param argument="random_state" type="integer" value="0" label="Numpy random seed"/>
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348 <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']"/>
0
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349 </when>
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350 <when value="tl.score_genes">
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351 <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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352 <expand macro="sanitize_query"/>
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353 </param>
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354 <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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355 <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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356 <expand macro="sanitize_query"/>
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357 </param>
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358 <param argument="score_name" type="text" value="score" label="Name of the field to be added in '.obs'">
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359 <expand macro="sanitize_query"/>
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360 </param>
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361 <expand macro="params_score_genes"/>
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362 </when>
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363 <when value="tl.score_genes_cell_cycle">
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364 <conditional name='s_genes'>
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365 <param name="format" type="select" label="Format for the list of genes associated with S phase">
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366 <option value="text" selected="true">Text</option>
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367 <option value="file">File</option>
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368 </param>
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369 <when value="text">
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370 <param name="text" type="text" value="" label="List of genes associated with S phase" help="Genes separated by a comma">
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371 <expand macro="sanitize_query"/>
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372 </param>
1
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373 </when>
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374 <when value="file">
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375 <param name="file" type="data" format="txt" label="File with the list of genes associated with S phase" help="One gene per line"/>
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376 </when>
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377 </conditional>
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378 <conditional name='g2m_genes'>
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379 <param name="format" type="select" label="Format for the list of genes associated with G2M phase">
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380 <option value="text" selected="true">Text</option>
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381 <option value="file">File</option>
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382 </param>
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383 <when value="text">
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384 <param name="text" type="text" value="" label="List of genes associated with G2M phase" help="Genes separated by a comma">
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385 <expand macro="sanitize_query"/>
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386 </param>
1
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387 </when>
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388 <when value="file">
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389 <param name="file" type="data" format="txt" label="File with the list of genes associated with G2M phase" help="One gene per line"/>
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390 </when>
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391 </conditional>
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392 <expand macro="params_score_genes"/>
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393 </when>
1
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394 <when value="tl.rank_genes_groups">
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395 <param argument="groupby" type="text" value="" label="The key of the observations grouping to consider">
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396 <expand macro="sanitize_query"/>
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397 </param>
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398 <expand macro="param_use_raw"/>
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399 <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.">
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400 <expand macro="sanitize_query"/>
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401 </param>
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402 <param argument="layer" type="text" value="" label="Key from adata.layers whose value will be used to perform tests on">
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403 <expand macro="sanitize_query"/>
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404 </param>
1
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405 <conditional name="ref">
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406 <param name="rest" type="select" label="Comparison">
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407 <option value="rest" selected="true">Compare each group to the union of the rest of the group</option>
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408 <option value="group_id">Compare with respect to a specific group</option>
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409 </param>
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410 <when value="rest"/>
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411 <when value="group_id">
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412 <param argument="reference" type="text" value="" label="Group identifier with respect to which compare">
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413 <expand macro="sanitize_query"/>
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414 </param>
1
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415 </when>
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416 </conditional>
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417 <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"/>
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418 <conditional name="tl_rank_genes_groups_method">
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419 <param argument="method" type="select" label="Method">
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420 <option value="t-test" selected="true">t-test</option>
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421 <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
422 <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
423 <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
424 </param>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
425 <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
426 <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
427 </when>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
428 <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
429 <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
430 <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
431 </when>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
432 <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
433 <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
434 </when>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
435 <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
436 <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
437 <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
438 <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
439 <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
440 <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
441 <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
442 <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
443 </param>
17
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iuc
parents: 15
diff changeset
444 <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
445 <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
446 <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
447 <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
448 <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
449 </when>
17
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iuc
parents: 15
diff changeset
450 <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
451 <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
452 <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
453 <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
454 <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
455 </when>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
456 <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
457 <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
458 <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
459 <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
460 <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
461 <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
462 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
463 </when>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
464 </conditional>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
465 <conditional name="intercept_scaling">
17
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iuc
parents: 15
diff changeset
466 <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
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parents: 15
diff changeset
467 <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
468 <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
469 </param>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
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470 <when value="True">
17
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iuc
parents: 15
diff changeset
471 <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
472 </when>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
473 <when value="False"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
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474 </conditional>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
475 <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
476 </when>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
477 <when value="sag">
17
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iuc
parents: 15
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478 <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
479 <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
480 <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
481 <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
482 <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
483 </when>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
484 <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
485 <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
486 <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
487 <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
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488 <option value="None">None</option>
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iuc
parents: 15
diff changeset
489 </expand>
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
490 <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
491 <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
492 <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
493 <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
494 </conditional>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
495 <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
496 <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
497 </when>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
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498 </conditional>
17
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parents: 15
diff changeset
499 <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
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parents: 15
diff changeset
500 <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
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501 </when>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
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502 </conditional>
17
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 15
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503 <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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504 </when>
11
6bd82ed14acd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
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parents: 10
diff changeset
505 <!-- With inplace=True, NotImplementedError: Writing Pandas dataframes to h5ad is currently under development. Please use `inplace=False`. -->
17
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parents: 15
diff changeset
506 <!-- Issue is fixed in the script -->
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diff changeset
507 <when value="tl.marker_gene_overlap">
1
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parents: 0
diff changeset
508 <repeat name="reference_markers" title="Marker genes">
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parents: 15
diff changeset
509 <param name="key" type="text" value="" label="Cell identity name"/>
3
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parents: 2
diff changeset
510 <param name="values" type="text" value="" label="List of genes" help="Comma-separated names from 'var'"/>
1
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parents: 0
diff changeset
511 </repeat>
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parents: 0
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512 <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"
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parents: 0
diff changeset
513 <conditional name="overlap">
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
514 <param argument="method" type="select" label="Method to calculate marker gene overlap">
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diff changeset
515 <option value="overlap_count" selected="true">overlap_count: Intersection of the gene set</option>
1
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parents: 0
diff changeset
516 <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"
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parents: 0
diff changeset
517 <option value="jaccard">jaccard: Jaccard index</option>
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parents: 0
diff changeset
518 </param>
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parents: 0
diff changeset
519 <when value="overlap_count">
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
520 <param argument="normalize" type="select" label="Normalization option for the marker gene overlap output">
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521 <option value="None" selected="true">None</option>
1
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parents: 0
diff changeset
522 <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"
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parents: 0
diff changeset
523 <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"
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parents: 0
diff changeset
524 </param>
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parents: 0
diff changeset
525 </when>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
526 <when value="overlap_coef"/>
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parents: 0
diff changeset
527 <when value="jaccard"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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528 </conditional>
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diff changeset
529 <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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diff changeset
530 <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: 15
diff changeset
531 <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
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parents: 15
diff changeset
532 </when>
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parents: 15
diff changeset
533 <when value="pp.log1p">
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parents: 15
diff changeset
534 <param argument="base" type="integer" value="" optional="true" label="Base of the logarithm." help="Natural logarithm is used by default."/>
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535 <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
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parents: 15
diff changeset
536 <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: 15
diff changeset
537 </param>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 15
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538 <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
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parents: 15
diff changeset
539 <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: 15
diff changeset
540 </param>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 15
diff changeset
541 </when>
1
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parents: 0
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542 <when value="pp.scale">
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18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 15
diff changeset
543 <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: 15
diff changeset
544 <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
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parents: 15
diff changeset
545 <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
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parents: 15
diff changeset
546 <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: 15
diff changeset
547 </param>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 15
diff changeset
548 <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
parents: 15
diff changeset
549 <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: 15
diff changeset
550 </param>
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diff changeset
551 <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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parents: 15
diff changeset
552 <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: 15
diff changeset
553 </param>
1
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parents: 0
diff changeset
554 </when>
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parents: 0
diff changeset
555 <when value="pp.sqrt"/>
0
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556 </conditional>
6
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parents: 5
diff changeset
557 <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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diff changeset
558 </inputs>
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
559 <outputs>
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
560 <expand macro="anndata_outputs"/>
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
561 </outputs>
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
562 <tests>
18
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diff changeset
563 <!-- test 1 -->
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parents: 10
diff changeset
564 <test expect_num_outputs="2">
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parents: 15
diff changeset
565 <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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parents:
diff changeset
566 <conditional name="method">
1
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parents: 0
diff changeset
567 <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"
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parents: 0
diff changeset
568 <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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parents:
diff changeset
569 </conditional>
6
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parents: 5
diff changeset
570 <section name="advanced_common">
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parents: 15
diff changeset
571 <param name="show_log" value="true"/>
6
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parents: 5
diff changeset
572 </section>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
573 <output name="hidden_output">
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
574 <assert_contents>
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parents: 15
diff changeset
575 <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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parents: 15
diff changeset
576 <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
577 <has_text_matching expression="var_type='genes'"/>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 15
diff changeset
578 <has_text_matching expression="qc_vars=\['mito', 'negative'\]"/>
6
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parents: 5
diff changeset
579 </assert_contents>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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parents: 5
diff changeset
580 </output>
17
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parents: 15
diff changeset
581 <output name="anndata_out" ftype="h5ad">
6
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parents: 5
diff changeset
582 <assert_contents>
17
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parents: 15
diff changeset
583 <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
584 <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
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diff changeset
585 </assert_contents>
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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586 </output>
1
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iuc
parents: 0
diff changeset
587 </test>
17
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
588
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
589 <!-- test 2 -->
11
6bd82ed14acd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
590 <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
591 <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
592 <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
593 <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
594 <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
595 <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
596 </conditional>
ca086f24422f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
597 <section name="advanced_common">
ca086f24422f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
598 <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: 14
diff changeset
599 </section>
ca086f24422f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
600 <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
601 <assert_contents>
ca086f24422f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
602 <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
603 <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
604 <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
605 <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
606 <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
607 </assert_contents>
ca086f24422f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
608 </output>
17
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
609 <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
610 <assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
611 <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
612 <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
613 </assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
614 </output>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
615 </test>
18
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
616
17
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
617 <!-- test 3 -->
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
618 <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
619 <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
620 <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
621 <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
622 </conditional>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
623 <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
624 <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
625 </section>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
626 <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
627 <assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
628 <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
629 <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
630 <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
631 <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
632 <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: 15
diff changeset
633 <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: 15
diff changeset
634 </assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
635 </output>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
636 <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
637 <assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
638 <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: 15
diff changeset
639 <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
640 </assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
641 </output>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
642 </test>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
643
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
644 <!-- test 4 -->
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
645 <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
646 <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
647 <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
648 <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
649 <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: 15
diff changeset
650 <param name="metric" value="braycurtis"/>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
651 </conditional>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
652 <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
653 <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
654 </section>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
655 <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
656 <assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
657 <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
658 <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
659 <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
660 <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
661 <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
662 <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
663 </assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
664 </output>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
665 <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
666 <assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
667 <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
668 </assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
669 </output>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
670 </test>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
671
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
672 <!-- test 5 -->
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
673 <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
674 <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
675 <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
676 <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
677 <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
678 <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
679 <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
680 <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
681 </conditional>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
682 <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
683 <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
684 </section>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
685 <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
686 <assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
687 <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
688 <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
689 <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
690 <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
691 <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
692 <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
693 <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
694 <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
695 </assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
696 </output>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
697 <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
698 <assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
699 <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
700 </assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
701 </output>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
702 </test>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
703
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
704 <!-- test 6 -->
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
705 <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
706 <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
707 <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
708 <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
709 <conditional name='s_genes'>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
710 <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
711 <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
712 </conditional>
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='g2m_genes'>
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="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
715 <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
716 </conditional>
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="1"/>
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_cell_cycle"/>
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="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
727 <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
728 <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
729 <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: 15
diff changeset
730 <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
731 </assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
732 </output>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
733 <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
734 <assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
735 <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: 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 </output>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
738 </test>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
739
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
740 <!-- test 7 -->
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
741 <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
742 <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
743 <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
744 <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
745 <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
746 <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
747 <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
748 <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
749 </conditional>
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 <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
752 <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
753 </section>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
754 <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
755 <assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
756 <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
757 <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
758 <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
759 <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
760 <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
761 <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
762 <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
763 </assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
764 </output>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
765 <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
766 <assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
767 <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
768 </assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
769 </output>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
770 </test>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
771
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
772 <!-- test 8 -->
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
773 <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
774 <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
775 <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
776 <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
777 <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
778 <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
779 <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
780 <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
781 </conditional>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
782 </conditional>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
783 <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
784 <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
785 </section>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
786 <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
787 <assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
788 <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
789 <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
790 <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
791 <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
792 <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
793 <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
794 <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
795 <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
796 <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
797 <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
798 <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
799 <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
800 <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
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 9 -->
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 name="solver">
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
820 <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
821 <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
822 <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
823 <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
824 </conditional>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
825 </conditional>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
826 </conditional>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
827 </conditional>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
828 <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
829 <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
830 </section>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
831 <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
832 <assert_contents>
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="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
834 <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
835 <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
836 <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
837 <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
838 <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
839 <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
840 <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
841 <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
842 <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
843 <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: 15
diff changeset
844 <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
845 <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
846 </assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
847 </output>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
848 <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
849 <assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
850 <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
851 </assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
852 </output>
18
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
853 </test>
17
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
854
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
855 <!-- test 10 -->
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
856 <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: 17
diff changeset
857 <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: 17
diff changeset
858 <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
859 <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
860 <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: 17
diff changeset
861 <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
862 <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
863 <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: 17
diff changeset
864 <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
865 </conditional>
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
866 <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
867 <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
868 <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
869 <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
870 <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
871 <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
872 <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
873 <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
874 </conditional>
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
875 </conditional>
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
876 </conditional>
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
877 </conditional>
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
878 <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
879 <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
880 </section>
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
881 <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
882 <assert_contents>
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
883 <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
884 <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
885 <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
886 <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
887 <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
888 <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
889 <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
890 <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
891 <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
892 <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
893 <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
894 <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
895 <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
896 <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
897 </assert_contents>
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
898 </output>
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
899 <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
900 <assert_contents>
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
901 <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
902 </assert_contents>
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
903 </output>
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
904 </test>
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
905
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
906 <!-- test 11 -->
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
907 <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
908 <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
909 <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
910 <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
911 <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
912 <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
913 <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
914 </repeat>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
915 <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
916 <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
917 <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
918 </repeat>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
919 <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
920 <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
921 <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
922 </repeat>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
923 </conditional>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
924 <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
925 <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
926 </section>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
927 <assert_stdout>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
928 <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
929 </assert_stdout>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
930 <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
931 <assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
932 <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
933 </assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
934 </output>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
935 <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
936 <assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
937 <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
938 </assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
939 </output>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
940 </test>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
941
18
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
942 <!-- 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
943 <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
944 <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
945 <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
946 <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
947 </conditional>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
948 <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
949 <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
950 </section>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
951 <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
952 <assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
953 <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: 15
diff changeset
954 </assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
955 </output>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
956 <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
957 <assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
958 <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: 15
diff changeset
959 </assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
960 </output>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
961 </test>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
962
18
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
963 <!-- test 13 -->
17
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
964 <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
965 <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
966 <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
967 <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
968 </conditional>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
969 <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
970 <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
971 </section>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
972 <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
973 <assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
974 <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
975 <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
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 <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
979 <assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
980 <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
981 </assert_contents>
18
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
982 </output>
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
983 </test>
17
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
984
18
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
985 <!-- 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
986 <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
987 <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
988 <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
989 <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
990 <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
991 </conditional>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
992 <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
993 <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
994 </section>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
995 <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
996 <assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
997 <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
998 <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
999 <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
1000 </assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
1001 </output>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
1002 <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
1003 <assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
1004 <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
1005 </assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
1006 </output>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
1007 </test>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
1008
18
d1cd8c147809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
iuc
parents: 17
diff changeset
1009 <!-- 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
1010 <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
1011 <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
1012 <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
1013 <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
1014 </conditional>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
1015 <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
1016 <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
1017 </section>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
1018 <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
1019 <assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
1020 <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
1021 <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
1022 <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
1023 </assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
1024 </output>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
1025 <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
1026 <assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
1027 <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
1028 </assert_contents>
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
1029 </output>
15
ca086f24422f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
1030 </test>
0
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1031 </tests>
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
1032 <help><![CDATA[
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1033 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
parents: 0
diff changeset
1034 ===================================================================
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1035
17
18262103fa61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 15
diff changeset
1036 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 changeset
1037 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 changeset
1038
3
cc0deb593fc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
1039 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 changeset
1040
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
1041 - 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
1042 - 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 changeset
1043 - 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)
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diff changeset
1044 - 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)
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diff changeset
1045 - 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
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diff changeset
1046
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diff changeset
1047 And also the variable level metrics:
0
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diff changeset
1048
1
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diff changeset
1049 - total_{expr_type} (e.g. "total_counts", sum of counts for a gene)
3
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parents: 2
diff changeset
1050 - mean_{expr_type} (e.g. "mean counts", mean expression over all cells)
1
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diff changeset
1051 - 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"
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diff changeset
1052 - 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"
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parents: 0
diff changeset
1053
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diff changeset
1054 More details on the `scanpy documentation
14
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diff changeset
1055 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.calculate_qc_metrics.html>`__
1
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diff changeset
1056
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diff changeset
1057 Compute a neighborhood graph of observations, using `pp.neighbors`
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diff changeset
1058 ==================================================================
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diff changeset
1059
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diff changeset
1060 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"
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diff changeset
1061 which also provides a method for estimating connectivities of data points -
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diff changeset
1062 the connectivity of the manifold (`method=='umap'`). If `method=='diffmap'`,
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diff changeset
1063 connectivities are computed according to Coifman et al (2005), in the adaption of
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diff changeset
1064 Haghverdi et al (2016).
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diff changeset
1065
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diff changeset
1066 The returned AnnData object contains:
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diff changeset
1067
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1068 - Weighted adjacency matrix of the neighborhood graph of data points (connectivities). Weights should be interpreted as connectivities.
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diff changeset
1069 - Distances for each pair of neighbors (distances)
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diff changeset
1070
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diff changeset
1071 This data are stored in the unstructured annotation (uns) and can be accessed using the inspect tool for AnnData objects
0
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1072
1
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1073 More details on the `scanpy documentation
14
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1074 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.neighbors.html>`__
1
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diff changeset
1075
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diff changeset
1076 Score a set of genes, using `tl.score_genes`
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1077 ============================================
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1078
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1079 The score is the average expression of a set of genes subtracted with the
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1080 average expression of a reference set of genes. The reference set is
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1081 randomly sampled from the `gene_pool` for each binned expression value.
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diff changeset
1082
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diff changeset
1083 This reproduces the approach in Seurat (Satija et al, 2015) and has been implemented
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1084 for Scanpy by Davide Cittaro.
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1085
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1086 More details on the `scanpy documentation
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1087 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.score_genes.html>`__
1
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1088
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1089 Score cell cycle genes, using `tl.score_genes_cell_cycle`
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1090 =========================================================
0
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1091
1
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1092 Given two lists of genes associated to S phase and G2M phase, calculates
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1093 scores and assigns a cell cycle phase (G1, S or G2M). See
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1094 `score_genes` for more explanation.
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1095
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1096 More details on the `scanpy documentation
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1097 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.score_genes_cell_cycle.html>`__
1
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1098
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1099 Rank genes for characterizing groups, using `tl.rank_genes_groups`
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1100 ==================================================================
0
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1101
1
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1102 The returned AnnData object contains:
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1103
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1104 - Gene names, ordered according to scores
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1105 - 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"
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1106 - 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.
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1107 - P-values
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1108 - Ajusted p-values
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1109
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1110 This data are stored in the unstructured annotation (uns) and can be accessed using the inspect tool for AnnData objects
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1111
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1112 More details on the `scanpy documentation
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1113 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.rank_genes_groups.html>`__
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1114
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1115
1
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1116 Calculate an overlap score between data-deriven marker genes and provided markers (`tl.marker_gene_overlap`)
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1117 ============================================================================================================
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1118
1
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1119 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.
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1120
17
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1121 More details on the `scanpy documentation
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1122 <https://scanpy.readthedocs.io/en/stable/generated/scanpy.tl.marker_gene_overlap.html>`__
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1123
1
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1124 Logarithmize the data matrix (`pp.log1p`)
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1125 =========================================
0
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1126
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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1127 More details on the `scanpy documentation
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f54f0f0598ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
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1128 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.log1p.html>`__
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1129
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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1130 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"
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1131 ======================================================
0
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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1132
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a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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1133 More details on the `scanpy documentation
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f54f0f0598ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
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1134 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.scale.html>`__
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1135
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a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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1136 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"
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1137 ====================================================
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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1138
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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1139 `X = sqrt(X)`
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1140 ]]></help>
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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1141 <expand macro="citations"/>
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5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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1142 </tool>