Mercurial > repos > iuc > scanpy_inspect

annotate inspect.xml @ 7:6c145a6868cc draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
author iuc
date Wed, 20 May 2020 16:10:30 -0400
parents 5e9171dc8244
children 9d33775ec67d
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7d22964a8639 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit e6675eff6b4d49386c2a9e4dde0011ba33aedbcc"
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1 <tool id="scanpy_inspect" name="Inspect and manipulate" version="@galaxy_version@" profile="@profile@">
1
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2 <description> with scanpy</description>
0
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3 <macros>
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4 <import>macros.xml</import>
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5 <xml name="score_genes_params">
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6 <param argument="n_bins" type="integer" value="25" label="Number of expression level bins for sampling" help=""/>
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7 <param argument="random_state" type="integer" value="0" label="Random seed for sampling" help=""/>
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8 <expand macro="param_use_raw"/>
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9 </xml>
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10 <token name="@CMD_score_genes_inputs@"><![CDATA[
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11 n_bins=$method.n_bins,
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12 random_state=$method.random_state,
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13 use_raw=$method.use_raw,
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14 copy=False
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15 ]]></token>
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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">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"
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24 label="Should a constant (a.k.a. bias or intercept) be added to the decision function?" help=""/>
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25 </xml>
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26 <xml name="max_iter">
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27 <param argument="max_iter" type="integer" min="0" value="100" label="Maximum number of iterations taken for the solvers to converge" help=""/>
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28 </xml>
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29 <xml name="multi_class">
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30 <param argument="multi_class" type="select" label="Multi class" help="">
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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 <option value="auto">auto: selects ‘ovr’ if the data is binary and otherwise selects ‘multinomial’</option>
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34 </param>
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35 </xml>
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36 <xml name="penalty">
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37 <param argument="penalty" type="select" label="Norm used in the penalization" help="">
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38 <option value="l1">l1</option>
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39 <option value="l2">l2</option>
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40 <option value="customized">customized</option>
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41 </param>
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42 </xml>
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43 <xml name="custom_penalty">
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44 <param argument="pen" type="text" value="" label="Norm used in the penalization" help="">
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45 <expand macro="sanitize_query" />
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46 </param>
1
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47 </xml>
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48 <xml name="random_state">
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49 <param argument="random_state" type="integer" value="" optional="true"
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50 label="The seed of the pseudo random number generator to use when shuffling the data" help=""/>
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51 </xml>
0
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52 </macros>
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53 <expand macro="requirements"/>
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54 <expand macro="version_command"/>
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55 <command detect_errors="exit_code"><![CDATA[
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56 @CMD@
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57 ]]></command>
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58 <configfiles>
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59 <configfile name="script_file"><![CDATA[
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60 @CMD_imports@
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61 @CMD_read_inputs@
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62
1
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63 #if $method.method == "pp.calculate_qc_metrics"
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64 sc.pp.calculate_qc_metrics(
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65 adata=adata,
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66 expr_type='$method.expr_type',
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67 var_type='$method.var_type',
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68 #if str($method.qc_vars) != ''
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69 #set $qc_vars = [str(x.strip()) for x in str($method.qc_vars).split(',')]
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70 qc_vars=$qc_vars,
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71 #end if
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72 #if str($method.percent_top) != ''
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73 #set $percent_top = [int(x.strip()) for x in str($method.percent_top).split(',')]
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74 percent_top=$method.percent_top,
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75 #end if
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76 inplace=True)
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77
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78 #else if $method.method == "tl.score_genes"
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79 sc.tl.score_genes(
0
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80 adata=adata,
1
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81 #set $gene_list = [str(x.strip()) for x in str($method.gene_list).split(',')]
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82 gene_list=$gene_list,
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83 ctrl_size=$method.ctrl_size,
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parents: 0
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84 score_name='$method.score_name',
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
85 #if $method.gene_pool
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iuc
parents: 0
diff changeset
86 #set $gene_pool = [str(x.strip()) for x in $method.gene_pool.split(',')]
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
87 gene_pool=$gene_pool,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
88 #end if
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
89 @CMD_score_genes_inputs@)
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
90
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
91 #else if $method.method == "tl.score_genes_cell_cycle"
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
92 #if str($method.s_genes.format) == 'file'
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
93 with open('$method.s_genes.file', 'r') as s_genes_f:
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
94 s_genes = [str(x.strip()) for x in s_genes_f.readlines()]
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
95 print(s_genes)
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
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96 #end if
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
97
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
98 #if str($method.g2m_genes.format) == 'file'
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
99 with open('$method.g2m_genes.file', 'r') as g2m_genes_f:
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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diff changeset
100 g2m_genes = [str(x.strip()) for x in g2m_genes_f.readlines()]
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
101 print(g2m_genes)
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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102 #end if
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
103
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
104 sc.tl.score_genes_cell_cycle(
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
105 adata=adata,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
106 #if str($method.s_genes.format) == 'text'
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iuc
parents: 0
diff changeset
107 #set $s_genes = [str(x.strip()) for x in $method.s_genes.text.split(',')]
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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108 s_genes=$s_genes,
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iuc
parents: 0
diff changeset
109 #else if str($method.s_genes.format) == 'file'
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
110 s_genes=s_genes,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
111 #end if
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
112 #if str($method.g2m_genes.format) == 'text'
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
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113 #set $g2m_genes = [str(x.strip()) for x in $method.g2m_genes.text.split(',')]
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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114 g2m_genes=$g2m_genes,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
115 #else if str($method.g2m_genes.format) == 'file'
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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116 g2m_genes=g2m_genes,
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iuc
parents: 0
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117 #end if
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iuc
parents: 0
diff changeset
118 @CMD_score_genes_inputs@)
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
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119
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
120 #else if $method.method == 'pp.neighbors'
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iuc
parents: 0
diff changeset
121 sc.pp.neighbors(
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iuc
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122 adata=adata,
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iuc
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123 n_neighbors=$method.n_neighbors,
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iuc
parents: 0
diff changeset
124 #if str($method.n_pcs) != ''
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iuc
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125 n_pcs=$method.n_pcs,
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iuc
parents: 0
diff changeset
126 #end if
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iuc
parents: 0
diff changeset
127 #if str($method.use_rep) != ''
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iuc
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128 use_rep='$method.use_rep',
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iuc
parents: 0
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129 #end if
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iuc
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130 knn=$method.knn,
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iuc
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131 random_state=$method.random_state,
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iuc
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132 method='$method.pp_neighbors_method',
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iuc
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133 metric='$method.metric',
0
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iuc
parents:
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134 copy=False)
1
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iuc
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135
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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diff changeset
136 #else if $method.method == 'tl.rank_genes_groups'
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iuc
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137 sc.tl.rank_genes_groups(
0
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iuc
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138 adata=adata,
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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139 groupby='$method.groupby',
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iuc
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140 #if str($method.groups) != ''
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iuc
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141 #set $group=[x.strip() for x in str($method.groups).split(',')]
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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142 groups=$group,
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iuc
parents: 0
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143 #end if
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iuc
parents: 0
diff changeset
144 #if $method.ref.rest == 'rest'
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iuc
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145 reference='$method.ref.rest',
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iuc
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146 #else
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iuc
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147 reference='$method.ref.reference',
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iuc
parents: 0
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148 #end if
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iuc
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149 n_genes=$method.n_genes,
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iuc
parents: 0
diff changeset
150 method='$method.tl_rank_genes_groups_method.method',
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iuc
parents: 0
diff changeset
151 #if $method.tl_rank_genes_groups_method.method != 'logreg'
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iuc
parents: 0
diff changeset
152 corr_method='$method.tl_rank_genes_groups_method.corr_method',
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iuc
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153 #else
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iuc
parents: 0
diff changeset
154 solver='$method.tl_rank_genes_groups_method.solver.solver',
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
155 #if $method.tl_rank_genes_groups_method.solver.solver == 'newton-cg'
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
156 penalty='l2',
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iuc
parents: 0
diff changeset
157 fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
158 max_iter=$method.tl_rank_genes_groups_method.solver.max_iter,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
159 multi_class='$method.tl_rank_genes_groups_method.solver.multi_class',
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
160 #else if $method.tl_rank_genes_groups_method.solver.solver == 'lbfgs'
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
161 penalty='l2',
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iuc
parents: 0
diff changeset
162 fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
163 max_iter=$method.tl_rank_genes_groups_method.solver.max_iter,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
164 multi_class='$method.tl_rank_genes_groups_method.solver.multi_class',
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
165 #else if $method.tl_rank_genes_groups_method.solver.solver == 'liblinear'
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iuc
parents: 0
diff changeset
166 #if $method.tl_rank_genes_groups_method.solver.penalty.penalty == 'l1'
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
167 penalty='l1',
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
168 #else if $method.tl_rank_genes_groups_method.solver.penalty.penalty == 'l2'
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
169 penalty='l2',
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
170 dual=$method.tl_rank_genes_groups_method.solver.penalty.dual,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
171 #else
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
172 penalty='$method.tl_rank_genes_groups_method.solver.penalty.pen',
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
173 #end if
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
174 fit_intercept=$method.tl_rank_genes_groups_method.solver.intercept_scaling.fit_intercept,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
175 #if $method.tl_rank_genes_groups_method.solver.intercept_scaling.fit_intercept == 'True'
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
176 intercept_scaling=$method.tl_rank_genes_groups_method.solver.intercept_scaling.intercept_scaling,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
177 #end if
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
178 #if $method.tl_rank_genes_groups_method.solver.random_state
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
179 random_state=$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"
iuc
parents: 0
diff changeset
180 #end if
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
181 #else if $method.tl_rank_genes_groups_method.solver.solver == 'sag'
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
182 penalty='l2',
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
183 fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
184 #if $method.tl_rank_genes_groups_method.solver.random_state
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
185 random_state=$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"
iuc
parents: 0
diff changeset
186 #end if
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
187 max_iter=$method.tl_rank_genes_groups_method.solver.max_iter,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
188 multi_class='$method.tl_rank_genes_groups_method.solver.multi_class',
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
189 #else if $method.tl_rank_genes_groups_method.solver.solver == 'saga'
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
190 #if $method.tl_rank_genes_groups_method.solver.penalty.penalty == 'l1'
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
191 penalty='l1',
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
192 #else if $method.tl_rank_genes_groups_method.solver.penalty.penalty == 'l2'
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
193 penalty='l2',
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
194 #else
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
195 penalty='$method.tl_rank_genes_groups_method.solver.penalty.pen',
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
196 #end if
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
197 fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
198 multi_class='$method.tl_rank_genes_groups_method.solver.multi_class',
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
199 #end if
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
200 tol=$method.tl_rank_genes_groups_method.tol,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
201 C=$method.tl_rank_genes_groups_method.c,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
202 #end if
3
cc0deb593fc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
203 use_raw=$method.use_raw)
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
204
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
205 #else if $method.method == "tl.marker_gene_overlap"
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
206 reference_markers = {}
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
207 #for $i, $s in enumerate($method.reference_markers)
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
208 #set $list=[x.strip() for x in str($s.values).split(',')]
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
209 reference_markers['$s.key'] = $list
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
210 #end for
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
211
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
212 sc.tl.marker_gene_overlap(
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
213 adata,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
214 reference_markers,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
215 #if str($method.key) != ''
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
216 key='$method.key',
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
217 #end if
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
218 method='$method.overlap.method',
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
219 #if $method.overlap.method == 'overlap_count' and str($method.overlap.normalize) != 'None'
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
220 normalize='$method.overlap.normalize',
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
221 #end if
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
222 #if str($method.top_n_markers) != ''
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
223 top_n_markers=$method.top_n_markers,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
224 #end if
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
225 #if str($method.adj_pval_threshold) != ''
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
226 adj_pval_threshold=$method.adj_pval_threshold,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
227 #end if
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
228 #if str($method.key_added) != ''
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
229 key_added='$method.key_added',
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
230 #end if
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
231 inplace=True)
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
232
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
233 #else if $method.method == "pp.log1p"
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
234 sc.pp.log1p(
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
235 data=adata,
0
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
236 copy=False)
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
237
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
238 #else if $method.method == "pp.scale"
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
239 sc.pp.scale(
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
240 data=adata,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
241 zero_center=$method.zero_center,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
242 #if $method.max_value
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
243 max_value=$method.max_value,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
244 #end if
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
245 copy=False)
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
246
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
247 #else if $method.method == "pp.sqrt"
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
248 sc.pp.sqrt(
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
249 data=adata,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
250 copy=False)
0
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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251 #end if
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252
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253 @CMD_anndata_write_outputs@
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254 ]]></configfile>
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255 </configfiles>
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256 <inputs>
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257 <expand macro="inputs_anndata"/>
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258 <conditional name="method">
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259 <param argument="method" type="select" label="Method used for inspecting">
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260 <option value="pp.calculate_qc_metrics">Calculate quality control metrics, using 'pp.calculate_qc_metrics'</option>
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261 <option value="pp.neighbors">Compute a neighborhood graph of observations, using 'pp.neighbors'</option>
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262 <option value="tl.score_genes">Score a set of genes, using 'tl.score_genes'</option>
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263 <option value="tl.score_genes_cell_cycle">Score cell cycle genes, using 'tl.score_genes_cell_cycle'</option>
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264 <option value="tl.rank_genes_groups">Rank genes for characterizing groups, using 'tl.rank_genes_groups'</option>
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265 <!--<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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266 <option value="pp.log1p">Logarithmize the data matrix, using 'pp.log1p'</option>
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267 <option value="pp.scale">Scale data to unit variance and zero mean, using 'pp.scale'</option>
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268 <option value="pp.sqrt">Square root the data matrix, using 'pp.sqrt'</option>
0
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269 </param>
1
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270 <when value="pp.calculate_qc_metrics">
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271 <param argument="expr_type" type="text" value="counts" label="Name of kind of values in X">
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272 <expand macro="sanitize_query" />
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273 </param>
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274 <param argument="var_type" type="text" value="genes" label="The kind of thing the variables are">
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275 <expand macro="sanitize_query" />
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276 </param>
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277 <param argument="qc_vars" type="text" 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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278 <expand macro="sanitize_query" />
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279 </param>
1
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280 <param argument="percent_top" type="text" value="" label="Proportions of top genes to cover"
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281 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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282 <expand macro="sanitize_vectors" />
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283 </param>
1
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284 </when>
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285 <when value="pp.neighbors">
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286 <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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287 <param argument="n_pcs" type="integer" min="0" value="" optional="true" label="Number of PCs to use" help=""/>
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288 <param argument="use_rep" type="text" value="" optional="true" label="Indicated representation to use" help="If not set, the representation is chosen automatically: for n_vars below 50, X is used, otherwise X_pca (uns) is used. If X_pca is not present, it's computed with default parameter">
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289 <expand macro="sanitize_query" />
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290 </param>
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291 <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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292 <param argument="random_state" type="integer" value="0" label="Numpy random seed" help=""/>
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293 <param name="pp_neighbors_method" argument="method" type="select" label="Method for computing connectivities" help="">
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294 <option value="umap">umap (McInnes et al, 2018)</option>
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295 <option value="gauss">gauss: Gauss kernel following (Coifman et al 2005) with adaptive width (Haghverdi et al 2016)</option>
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296 </param>
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297 <param argument="metric" type="select" label="Distance metric" help="">
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298 <expand macro="distance_metric_options"/>
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299 </param>
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300 </when>
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301 <when value="tl.score_genes">
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302 <param argument="gene_list" type="text" value="" label="The list of gene names used for score calculation" help="Genes separated by a comma">
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303 <expand macro="sanitize_query" />
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304 </param>
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305 <param argument="ctrl_size" type="integer" value="50" label="Number of reference genes to be sampled"
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306 help="If 'len(gene_list)' is not too low, you can set 'ctrl_size=len(gene_list)'."/>
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307 <param argument="gene_pool" type="text" value="" optional="true" label="Genes for sampling the reference set"
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308 help="Default is all genes. Genes separated by a comma">
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309 <expand macro="sanitize_query" />
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310 </param>
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311 <expand macro="score_genes_params"/>
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312 <param argument="score_name" type="text" value="score" label="Name of the field to be added in '.obs'" help="">
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313 <expand macro="sanitize_query" />
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314 </param>
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315 </when>
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316 <when value="tl.score_genes_cell_cycle">
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317 <conditional name='s_genes'>
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318 <param name="format" type="select" label="Format for the list of genes associated with S phase">
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319 <option value="file">File</option>
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320 <option value="text" selected="true">Text</option>
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321 </param>
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322 <when value="text">
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323 <param name="text" type="text" value="" label="List of genes associated with S phase" help="Genes separated by a comma">
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324 <expand macro="sanitize_query" />
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325 </param>
1
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326 </when>
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327 <when value="file">
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328 <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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329 </when>
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330 </conditional>
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331 <conditional name='g2m_genes'>
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parents: 0
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332 <param name="format" type="select" label="Format for the list of genes associated with G2M phase">
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parents: 0
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333 <option value="file">File</option>
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parents: 0
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334 <option value="text" selected="true">Text</option>
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parents: 0
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335 </param>
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parents: 0
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336 <when value="text">
7
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parents: 6
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337 <param name="text" type="text" value="" label="List of genes associated with G2M phase" help="Genes separated by a comma">
6c145a6868cc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
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parents: 6
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338 <expand macro="sanitize_query" />
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parents: 6
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339 </param>
1
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parents: 0
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340 </when>
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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341 <when value="file">
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parents: 0
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342 <param name="file" type="data" format="txt" label="File with the list of genes associated with G2M phase" help="One gene per line"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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343 </when>
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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344 </conditional>
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parents: 0
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345 <expand macro="score_genes_params"/>
0
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parents:
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346 </when>
1
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parents: 0
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347 <when value="tl.rank_genes_groups">
7
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parents: 6
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348 <param argument="groupby" type="text" value="" label="The key of the observations grouping to consider" help="">
6c145a6868cc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
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parents: 6
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349 <expand macro="sanitize_query" />
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parents: 6
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350 </param>
1
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parents: 0
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351 <expand macro="param_use_raw"/>
7
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parents: 6
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352 <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.">
6c145a6868cc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
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parents: 6
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353 <expand macro="sanitize_query" />
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parents: 6
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354 </param>
1
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parents: 0
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355 <conditional name="ref">
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parents: 0
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356 <param name="rest" type="select" label="Comparison">
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parents: 0
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357 <option value="rest">Compare each group to the union of the rest of the group</option>
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parents: 0
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358 <option value="group_id">Compare with respect to a specific group</option>
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parents: 0
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359 </param>
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parents: 0
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360 <when value="rest"/>
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parents: 0
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361 <when value="group_id">
7
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parents: 6
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362 <param argument="reference" type="text" value="" label="Group identifier with respect to which compare">
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parents: 6
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363 <expand macro="sanitize_query" />
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parents: 6
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364 </param>
1
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parents: 0
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365 </when>
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parents: 0
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366 </conditional>
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parents: 0
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367 <param argument="n_genes" type="integer" min="0" value="100" label="The number of genes that appear in the returned tables" help=""/>
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parents: 0
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368 <conditional name="tl_rank_genes_groups_method">
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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369 <param argument="method" type="select" label="Method">
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370 <option value="t-test">t-test</option>
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parents: 0
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371 <option value="wilcoxon">Wilcoxon-Rank-Sum</option>
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372 <option value="t-test_overestim_var" selected="true">t-test with overestimate of variance of each group</option>
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parents: 0
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373 <option value="logreg">Logistic regression</option>
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parents: 0
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374 </param>
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parents: 0
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375 <when value="t-test">
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parents: 0
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376 <expand macro="corr_method"/>
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parents: 0
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377 </when>
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parents: 0
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378 <when value="wilcoxon">
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parents: 0
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379 <expand macro="corr_method"/>
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parents: 0
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380 </when>
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parents: 0
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381 <when value="t-test_overestim_var">
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parents: 0
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382 <expand macro="corr_method"/>
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parents: 0
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383 </when>
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parents: 0
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384 <when value="logreg">
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parents: 0
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385 <conditional name="solver">
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parents: 0
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386 <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.">
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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387 <option value="newton-cg">newton-cg</option>
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parents: 0
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388 <option value="lbfgs">lbfgs</option>
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parents: 0
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389 <option value="liblinear">liblinear</option>
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parents: 0
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390 <option value="sag">sag</option>
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parents: 0
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391 <option value="saga">saga</option>
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parents: 0
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392 </param>
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parents: 0
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393 <when value="newton-cg">
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parents: 0
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394 <expand macro="fit_intercept"/>
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parents: 0
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395 <expand macro="max_iter"/>
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parents: 0
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396 <expand macro="multi_class"/>
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parents: 0
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397 </when>
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parents: 0
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398 <when value="lbfgs">
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iuc
parents: 0
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399 <expand macro="fit_intercept"/>
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iuc
parents: 0
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400 <expand macro="max_iter"/>
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iuc
parents: 0
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401 <expand macro="multi_class"/>
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parents: 0
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402 </when>
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parents: 0
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403 <when value="liblinear">
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iuc
parents: 0
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404 <conditional name="penalty">
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iuc
parents: 0
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405 <expand macro="penalty"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
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406 <when value="l1"/>
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parents: 0
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407 <when value="l2">
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parents: 0
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408 <param argument="dual" type="boolean" truevalue="True" falsevalue="False" checked="false"
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parents: 0
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409 label="Dual (not primal) formulation?" help="Prefer primal when n_samples > n_features"/>
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parents: 0
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410 </when>
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parents: 0
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411 <when value="customized">
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parents: 0
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412 <expand macro="custom_penalty"/>
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iuc
parents: 0
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413 </when>
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iuc
parents: 0
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414 </conditional>
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iuc
parents: 0
diff changeset
415 <conditional name="intercept_scaling">
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parents: 0
diff changeset
416 <param argument="fit_intercept" type="select"
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parents: 0
diff changeset
417 label="Should a constant (a.k.a. bias or intercept) be added to the decision function?" help="">
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
418 <option value="True">Yes</option>
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parents: 0
diff changeset
419 <option value="False">No</option>
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parents: 0
diff changeset
420 </param>
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parents: 0
diff changeset
421 <when value="True">
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parents: 0
diff changeset
422 <param argument="intercept_scaling" type="float" value="1.0"
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parents: 0
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423 label="Intercept scaling"
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parents: 0
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424 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."/>
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
425 </when>
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parents: 0
diff changeset
426 <when value="False"/>
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parents: 0
diff changeset
427 </conditional>
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parents: 0
diff changeset
428 <expand macro="random_state"/>
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parents: 0
diff changeset
429 </when>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
430 <when value="sag">
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iuc
parents: 0
diff changeset
431 <expand macro="fit_intercept"/>
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iuc
parents: 0
diff changeset
432 <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
433 <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
434 <expand macro="multi_class"/>
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
435 </when>
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parents: 0
diff changeset
436 <when value="saga">
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iuc
parents: 0
diff changeset
437 <conditional name="penalty">
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iuc
parents: 0
diff changeset
438 <expand macro="penalty"/>
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iuc
parents: 0
diff changeset
439 <when value="l1"/>
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parents: 0
diff changeset
440 <when value="l2"/>
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parents: 0
diff changeset
441 <when value="customized">
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parents: 0
diff changeset
442 <expand macro="custom_penalty"/>
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parents: 0
diff changeset
443 </when>
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parents: 0
diff changeset
444 </conditional>
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parents: 0
diff changeset
445 <expand macro="fit_intercept"/>
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parents: 0
diff changeset
446 <expand macro="multi_class"/>
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parents: 0
diff changeset
447 </when>
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parents: 0
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448 </conditional>
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parents: 0
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449 <param argument="tol" type="float" value="1e-4" label="Tolerance for stopping criteria" help=""/>
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parents: 0
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450 <param argument="c" type="float" value="1.0" label="Inverse of regularization strength"
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parents: 0
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451 help="It must be a positive float. Like in support vector machines, smaller values specify stronger regularization."/>
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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452 </when>
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parents: 0
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453 </conditional>
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parents: 0
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454 </when>
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parents: 0
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455 <!--<when value="tl.marker_gene_overlap">
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parents: 0
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456 <repeat name="reference_markers" title="Marker genes">
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parents: 0
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457 <param name="key" type="text" value="" label="Cell identity name" help=""/>
3
cc0deb593fc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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parents: 2
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458 <param name="values" type="text" value="" label="List of genes" help="Comma-separated names from 'var'"/>
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
459 </repeat>
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parents: 0
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460 <param argument="key" type="text" value="rank_genes_groups" label="Key in adata.uns where the rank_genes_groups output is stored"/>
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parents: 0
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461 <conditional name="overlap">
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parents: 0
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462 <param argument="method" type="select" label="Method to calculate marker gene overlap">
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parents: 0
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463 <option value="overlap_count">overlap_count: Intersection of the gene set</option>
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parents: 0
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464 <option value="overlap_coef">overlap_coef: Overlap coefficient</option>
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parents: 0
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465 <option value="jaccard">jaccard: Jaccard index</option>
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parents: 0
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466 </param>
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parents: 0
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467 <when value="overlap_count">
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parents: 0
diff changeset
468 <param argument="normalize" type="select" label="Normalization option for the marker gene overlap output">
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parents: 0
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469 <option value="None">None</option>
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parents: 0
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470 <option value="reference">reference: Normalization of the data by the total number of marker genes given in the reference annotation per group</option>
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parents: 0
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471 <option value="data">data: Normalization of the data by the total number of marker genes used for each cluster</option>
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parents: 0
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472 </param>
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parents: 0
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473 </when>
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iuc
parents: 0
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474 <when value="overlap_coef"/>
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parents: 0
diff changeset
475 <when value="jaccard"/>
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parents: 0
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476 </conditional>
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iuc
parents: 0
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477 <param argument="top_n_markers" type="integer" optional="true" 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."/>
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parents: 0
diff changeset
478 <param argument="adj_pval_threshold" type="float" optional="true" 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."/>
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parents: 0
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479 <param argument="key_added" type="text" value="" optional="true" label="Key that will contain the marker overlap scores in 'uns'"/>
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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480 </when>-->
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parents: 0
diff changeset
481 <when value="pp.log1p"/>
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parents: 0
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482 <when value="pp.scale">
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parents: 0
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483 <param argument="zero_center" type="boolean" truevalue="True" falsevalue="False" checked="true"
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parents: 0
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484 label="Zero center?" help="If not, it omits zero-centering variables, which allows to handle sparse input efficiently."/>
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parents: 0
diff changeset
485 <param argument="max_value" type="float" value="" optional="true" label="Maximum value"
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parents: 0
diff changeset
486 help="Clip (truncate) to this value after scaling. If not set, it does not clip."/>
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parents: 0
diff changeset
487 </when>
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parents: 0
diff changeset
488 <when value="pp.sqrt"/>
0
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parents:
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489 </conditional>
6
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parents: 5
diff changeset
490 <expand macro="inputs_common_advanced"/>
0
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parents:
diff changeset
491 </inputs>
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diff changeset
492 <outputs>
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parents:
diff changeset
493 <expand macro="anndata_outputs"/>
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parents:
diff changeset
494 </outputs>
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parents:
diff changeset
495 <tests>
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parents:
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496 <test>
6
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parents: 5
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497 <!-- test 0 -->
1
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parents: 0
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498 <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
iuc
parents:
diff changeset
499 <conditional name="method">
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
500 <param name="method" value="pp.calculate_qc_metrics"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
501 <param name="expr_type" value="counts"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
502 <param name="var_type" value="genes"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
503 <param name="qc_vars" value="mito,negative"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
504 <param name="percent_top" value=""/>
0
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
505 </conditional>
6
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
506 <section name="advanced_common">
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
507 <param name="show_log" value="true" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
508 </section>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
509 <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
510 <assert_contents>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
511 <has_text_matching expression="sc.pp.calculate_qc_metrics" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
512 <has_text_matching expression="expr_type='counts'" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
513 <has_text_matching expression="var_type='genes'" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
514 <has_text_matching expression="qc_vars=\['mito', 'negative'\]" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
515 </assert_contents>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
516 </output>
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
517 <output name="anndata_out" file="pp.calculate_qc_metrics.sparce_csr_matrix.h5ad" ftype="h5ad" compare="sim_size"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
518 </test>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
519 <test>
6
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
520 <!-- test 1 -->
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
521 <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad" />
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
522 <conditional name="method">
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
523 <param name="method" value="pp.neighbors"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
524 <param name="n_neighbors" value="15"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
525 <param name="knn" value="True"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
526 <param name="random_state" value="0"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
527 <param name="pp_neighbors_method" value="umap"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
528 <param name="metric" value="euclidean"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
529 </conditional>
6
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
530 <section name="advanced_common">
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
531 <param name="show_log" value="true" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
532 </section>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
533 <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
534 <assert_contents>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
535 <has_text_matching expression="sc.pp.neighbors"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
536 <has_text_matching expression="n_neighbors=15"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
537 <has_text_matching expression="knn=True"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
538 <has_text_matching expression="random_state=0"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
539 <has_text_matching expression="method='umap'"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
540 <has_text_matching expression="metric='euclidean'"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
541 </assert_contents>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
542 </output>
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
543 <output name="anndata_out" file="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size">
0
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
544 <assert_contents>
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
545 <has_h5_keys keys="X, obs, obsm, uns, var" />
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
546 </assert_contents>
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
547 </output>
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
548 </test>
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
549 <test>
6
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
550 <!-- test 2 -->
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
551 <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad" />
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
552 <conditional name="method">
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
553 <param name="method" value="pp.neighbors"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
554 <param name="n_neighbors" value="15"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
555 <param name="knn" value="True"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
556 <param name="pp_neighbors_method" value="gauss"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
557 <param name="metric" value="braycurtis"/>
0
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
558 </conditional>
6
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
559 <section name="advanced_common">
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
560 <param name="show_log" value="true" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
561 </section>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
562 <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
563 <assert_contents>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
564 <has_text_matching expression="sc.pp.neighbors"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
565 <has_text_matching expression="n_neighbors=15"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
566 <has_text_matching expression="knn=True"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
567 <has_text_matching expression="random_state=0"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
568 <has_text_matching expression="method='gauss'"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
569 <has_text_matching expression="metric='braycurtis'"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
570 </assert_contents>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
571 </output>
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
572 <output name="anndata_out" file="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
573 </test>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
574 <test>
6
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
575 <!-- test 3 -->
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
576 <param name="adata" value="krumsiek11.h5ad" />
0
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
577 <conditional name="method">
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
578 <param name="method" value="tl.score_genes"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
579 <param name="gene_list" value="Gata2, Fog1"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
580 <param name="ctrl_size" value="2"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
581 <param name="n_bins" value="2"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
582 <param name="random_state" value="2"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
583 <param name="use_raw" value="False"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
584 <param name="score_name" value="score"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
585 </conditional>
6
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
586 <section name="advanced_common">
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
587 <param name="show_log" value="true" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
588 </section>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
589 <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
590 <assert_contents>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
591 <has_text_matching expression="sc.tl.score_genes" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
592 <has_text_matching expression="gene_list=\['Gata2', 'Fog1'\]" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
593 <has_text_matching expression="ctrl_size=2" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
594 <has_text_matching expression="score_name='score'" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
595 <has_text_matching expression="n_bins=2" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
596 <has_text_matching expression="random_state=2" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
597 <has_text_matching expression="use_raw=False" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
598 <has_text_matching expression="copy=False" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
599 </assert_contents>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
600 </output>
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
601 <output name="anndata_out" file="tl.score_genes.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
602 </test>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
603 <test>
6
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
604 <!-- test 4 -->
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
605 <param name="adata" value="krumsiek11.h5ad" />
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
606 <conditional name="method">
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
607 <param name="method" value="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
608 <conditional name='s_genes'>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
609 <param name="format" value="text"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
610 <param name="text" value="Gata2, Fog1, EgrNab"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
611 </conditional>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
612 <conditional name='g2m_genes'>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
613 <param name="format" value="text"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
614 <param name="text" value="Gata2, Fog1, EgrNab"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
615 </conditional>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
616 <param name="n_bins" value="2"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
617 <param name="random_state" value="1"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
618 <param name="use_raw" value="False"/>
0
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
619 </conditional>
6
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
620 <section name="advanced_common">
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
621 <param name="show_log" value="true" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
622 </section>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
623 <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
624 <assert_contents>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
625 <has_text_matching expression="sc.tl.score_genes_cell_cycle"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
626 <has_text_matching expression="s_genes=\['Gata2', 'Fog1', 'EgrNab'\]"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
627 <has_text_matching expression="g2m_genes=\['Gata2', 'Fog1', 'EgrNab'\]"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
628 <has_text_matching expression="n_bins=2"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
629 <has_text_matching expression="random_state=1"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
630 <has_text_matching expression="use_raw=False"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
631 </assert_contents>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
632 </output>
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
633 <output name="anndata_out" file="tl.score_genes_cell_cycle.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
634 </test>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
635 <test>
6
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
636 <!-- test 5 -->
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
637 <param name="adata" value="krumsiek11.h5ad" />
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
638 <conditional name="method">
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
639 <param name="method" value="tl.rank_genes_groups"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
640 <param name="groupby" value="cell_type"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
641 <param name="use_raw" value="True"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
642 <conditional name="ref">
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
643 <param name="rest" value="rest"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
644 </conditional>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
645 <param name="n_genes" value="100"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
646 <conditional name="tl_rank_genes_groups_method">
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
647 <param name="method" 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
648 <param name="corr_method" value="benjamini-hochberg"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
649 </conditional>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
650 </conditional>
6
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
651 <section name="advanced_common">
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
652 <param name="show_log" value="true" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
653 </section>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
654 <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
655 <assert_contents>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
656 <has_text_matching expression="sc.tl.rank_genes_groups"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
657 <has_text_matching expression="groupby='cell_type'"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
658 <has_text_matching expression="use_raw=True"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
659 <has_text_matching expression="reference='rest'"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
660 <has_text_matching expression="n_genes=100"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
661 <has_text_matching expression="method='t-test_overestim_var'"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
662 <has_text_matching expression="corr_method='benjamini-hochberg'"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
663 </assert_contents>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
664 </output>
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
665 <output name="anndata_out" file="tl.rank_genes_groups.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
666 </test>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
667 <test>
6
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
668 <!-- test 6 -->
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
669 <param name="adata" value="pbmc68k_reduced.h5ad" />
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
670 <conditional name="method">
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
671 <param name="method" value="tl.rank_genes_groups"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
672 <param name="groupby" value="louvain"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
673 <param name="use_raw" value="True"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
674 <conditional name="ref">
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
675 <param name="rest" value="rest"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
676 </conditional>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
677 <param name="n_genes" value="100"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
678 <conditional name="tl_rank_genes_groups_method">
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
679 <param name="method" value="logreg"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
680 <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
681 <param name="solver" value="newton-cg"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
682 <param name="fit_intercept" value="True"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
683 <param name="max_iter" value="100"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
684 <param name="multi_class" value="auto"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
685 </conditional>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
686 <param name="tol" value="1e-4"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
687 <param name="c" value="1.0"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
688 </conditional>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
689 </conditional>
6
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
690 <section name="advanced_common">
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
691 <param name="show_log" value="true" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
692 </section>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
693 <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
694 <assert_contents>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
695 <has_text_matching expression="sc.tl.rank_genes_groups"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
696 <has_text_matching expression="groupby='louvain'"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
697 <has_text_matching expression="use_raw=True"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
698 <has_text_matching expression="reference='rest'"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
699 <has_text_matching expression="n_genes=100"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
700 <has_text_matching expression="method='logreg'"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
701 <has_text_matching expression="solver='newton-cg'"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
702 <has_text_matching expression="penalty='l2'"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
703 <has_text_matching expression="fit_intercept=True"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
704 <has_text_matching expression="max_iter=100"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
705 <has_text_matching expression="multi_class='auto'"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
706 <has_text_matching expression="tol=0.0001"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
707 <has_text_matching expression="C=1.0"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
708 </assert_contents>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
709 </output>
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
710 <output name="anndata_out" file="tl.rank_genes_groups.newton-cg.pbmc68k_reduced.h5ad" ftype="h5ad" compare="sim_size">
0
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
711 <assert_contents>
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
712 <has_h5_keys keys="X, obs, obsm, raw.X, raw.var, uns, var" />
0
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
713 </assert_contents>
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
714 </output>
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
715 </test>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
716 <test>
6
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
717 <!-- test 7 -->
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
718 <param name="adata" value="pbmc68k_reduced.h5ad" />
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
719 <conditional name="method">
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
720 <param name="method" value="tl.rank_genes_groups"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
721 <param name="groupby" value="louvain"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
722 <param name="use_raw" value="True"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
723 <conditional name="ref">
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
724 <param name="rest" value="rest"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
725 </conditional>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
726 <param name="n_genes" value="100"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
727 <conditional name="tl_rank_genes_groups_method">
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
728 <param name="method" value="logreg"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
729 <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
730 <param name="solver" value="liblinear"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
731 <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
732 <param name="penalty" value="l2"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
733 <param name="dual" value="False"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
734 <conditional name="intercept_scaling">
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
735 <param name="fit_intercept" value="True"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
736 <param name="intercept_scaling" value="1.0" />
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
737 </conditional>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
738 <param name="random_state" value="1"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
739 </conditional>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
740 </conditional>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
741 <param name="tol" value="1e-4"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
742 <param name="c" value="1.0"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
743 </conditional>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
744 </conditional>
6
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
745 <section name="advanced_common">
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
746 <param name="show_log" value="true" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
747 </section>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
748 <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
749 <assert_contents>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
750 <has_text_matching expression="sc.tl.rank_genes_groups"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
751 <has_text_matching expression="groupby='louvain'"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
752 <has_text_matching expression="use_raw=True"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
753 <has_text_matching expression="reference='rest'"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
754 <has_text_matching expression="n_genes=100"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
755 <has_text_matching expression="method='logreg'"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
756 <has_text_matching expression="solver='liblinear'"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
757 <has_text_matching expression="penalty='l2'"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
758 <has_text_matching expression="dual=False"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
759 <has_text_matching expression="fit_intercept=True"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
760 <has_text_matching expression="intercept_scaling=1.0"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
761 <has_text_matching expression="tol=0.0001"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
762 <has_text_matching expression="C=1.0"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
763 </assert_contents>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
764 </output>
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
765 <output name="anndata_out" file="tl.rank_genes_groups.liblinear.krumsiek11.h5ad" ftype="h5ad" compare="sim_size">
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
766 <assert_contents>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
767 <has_h5_keys keys="X, obs, obsm, raw.X, raw.var, uns, var" />
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
768 </assert_contents>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
769 </output>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
770 </test>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
771 <!--<test>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
772 < test 9 >
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
773 <param name="adata" value="tl.rank_genes_groups.louvain.neighbors.pca.pbmc68k_reduced.h5ad" />
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
774 <conditional name="method">
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
775 <param name="method" value="tl.marker_gene_overlap"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
776 <repeat name="reference_markers">
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
777 <param name="key" value="CD4 T cells"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
778 <param name="value" value="IL7R"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
779 </repeat>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
780 <repeat name="reference_markers">
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
781 <param name="key" value="CD14+ Monocytes"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
782 <param name="value" value="CD14,LYZ"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
783 </repeat>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
784 <repeat name="reference_markers">
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
785 <param name="key" value="B cells"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
786 <param name="value" value="MS4A1"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
787 </repeat>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
788 <conditional name="overlap">
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
789 <param argument="method" value="overlap_count"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
790 <param argument="normalize" value="None"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
791 </conditional>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
792 </conditional>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
793 <assert_stdout>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
794 <has_text_matching expression="tl.marker_gene_overlap"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
795 <has_text_matching expression="key='rank_genes_groups'"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
796 <has_text_matching expression="method='overlap_count'"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
797 </assert_stdout>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
798 <output name="anndata_out" file="pp.log1p.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
799 </test>-->
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
800 <test>
6
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
801 <!-- test 8 -->
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
802 <param name="adata" value="krumsiek11.h5ad" />
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
803 <conditional name="method">
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
804 <param name="method" value="pp.log1p"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
805 </conditional>
6
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
806 <section name="advanced_common">
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
807 <param name="show_log" value="true" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
808 </section>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
809 <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
810 <assert_contents>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
811 <has_text_matching expression="sc.pp.log1p"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
812 </assert_contents>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
813 </output>
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
814 <output name="anndata_out" file="pp.log1p.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
815 </test>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
816 <test>
6
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
817 <!-- test 9 -->
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
818 <param name="adata" value="krumsiek11.h5ad" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
819 <conditional name="method">
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
820 <param name="method" value="pp.scale"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
821 <param name="zero_center" value="true"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
822 </conditional>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
823 <section name="advanced_common">
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
824 <param name="show_log" value="true" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
825 </section>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
826 <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
827 <assert_contents>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
828 <has_text_matching expression="sc.pp.scale"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
829 <has_text_matching expression="zero_center=True"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
830 </assert_contents>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
831 </output>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
832 <output name="anndata_out" file="pp.scale.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
833 </test>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
834 <test>
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
835 <!-- test 10 -->
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
836 <param name="adata" value="krumsiek11.h5ad" />
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
837 <conditional name="method">
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
838 <param name="method" value="pp.scale"/>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
839 <param name="zero_center" value="true"/>
6
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
840 <param name="max_value" value="10"/>
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
841 </conditional>
6
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
842 <section name="advanced_common">
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
843 <param name="show_log" value="true" />
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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diff changeset
844 </section>
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diff changeset
845 <output name="hidden_output">
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parents: 5
diff changeset
846 <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
847 <has_text_matching expression="sc.pp.scale"/>
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
848 <has_text_matching expression="zero_center=True"/>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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diff changeset
849 <has_text_matching expression="max_value=10.0"/>
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
850 </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
851 </output>
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
852 <output name="anndata_out" file="pp.scale_max_value.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
1
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iuc
parents: 0
diff changeset
853 </test>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
854 <test>
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
855 <!-- test 11 -->
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
856 <param name="adata" value="krumsiek11.h5ad" />
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
857 <conditional name="method">
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
858 <param name="method" value="pp.sqrt"/>
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
859 </conditional>
6
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iuc
parents: 5
diff changeset
860 <section name="advanced_common">
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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diff changeset
861 <param name="show_log" value="true" />
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
862 </section>
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
863 <output name="hidden_output">
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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parents: 5
diff changeset
864 <assert_contents>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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865 <has_text_matching expression="sc.pp.sqrt"/>
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diff changeset
866 </assert_contents>
5e9171dc8244 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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867 </output>
1
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868 <output name="anndata_out" file="pp.sqrt.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
0
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diff changeset
869 </test>
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
870 </tests>
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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871 <help><![CDATA[
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
872 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"
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873 ===================================================================
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
874
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
875 Calculates a number of qc metrics for an AnnData object, largely based on calculateQCMetrics from scater.
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
876 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"
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parents: 0
diff changeset
877
3
cc0deb593fc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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parents: 2
diff changeset
878 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"
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parents: 0
diff changeset
879
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
880 - 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"
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parents: 0
diff changeset
881 - total_{expr_type} (e.g. "total_counts", total number of counts for a cell)
3
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882 - pct_{expr_type}_in_top_{n}_{var_type} - for n in percent_top (e.g. "pct_counts_in_top_50_genes", cumulative percentage of counts for 50 most expressed genes in a cell)
cc0deb593fc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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parents: 2
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883 - total_{expr_type}_{qc_var} - for qc_var in qc_vars (e.g. "total_counts_mito", total number of counts for variabes in qc_vars)
cc0deb593fc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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parents: 2
diff changeset
884 - 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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parents: 0
diff changeset
885
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
886 And also the variable level metrics:
0
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diff changeset
887
1
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
888 - total_{expr_type} (e.g. "total_counts", sum of counts for a gene)
3
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parents: 2
diff changeset
889 - mean_{expr_type} (e.g. "mean counts", mean expression over all cells)
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
890 - 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
891 - 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
892
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
893 More details on the `scanpy documentation
5
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diff changeset
894 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.calculate_qc_metrics.html>`__
1
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parents: 0
diff changeset
895
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
896 Compute a neighborhood graph of observations, using `pp.neighbors`
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
897 ==================================================================
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
898
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
899 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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parents: 0
diff changeset
900 which also provides a method for estimating connectivities of data points -
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
901 the connectivity of the manifold (`method=='umap'`). If `method=='diffmap'`,
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
902 connectivities are computed according to Coifman et al (2005), in the adaption of
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
903 Haghverdi et al (2016).
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
904
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
905 The returned AnnData object contains:
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
906
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
907 - Weighted adjacency matrix of the neighborhood graph of data points (connectivities). Weights should be interpreted as connectivities.
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
908 - Distances for each pair of neighbors (distances)
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
909
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
910 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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parents:
diff changeset
911
1
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
912 More details on the `scanpy documentation
5
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913 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.neighbors.html>`__
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parents: 0
diff changeset
914
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
915 Score a set of genes, using `tl.score_genes`
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
916 ============================================
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
917
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
918 The score is the average expression of a set of genes subtracted with the
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
919 average expression of a reference set of genes. The reference set is
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
920 randomly sampled from the `gene_pool` for each binned expression value.
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
921
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
922 This reproduces the approach in Seurat (Satija et al, 2015) and has been implemented
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
923 for Scanpy by Davide Cittaro.
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
924
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
925 More details on the `scanpy documentation
5
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parents: 3
diff changeset
926 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.score_genes.html>`__
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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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diff changeset
927
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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diff changeset
928 Score cell cycle genes, using `tl.score_genes_cell_cycle`
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
929 =========================================================
0
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930
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
931 Given two lists of genes associated to S phase and G2M phase, calculates
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
932 scores and assigns a cell cycle phase (G1, S or G2M). See
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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diff changeset
933 `score_genes` for more explanation.
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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diff changeset
934
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
935 More details on the `scanpy documentation
5
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diff changeset
936 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.score_genes_cell_cycle.html>`__
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
937
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
938 Rank genes for characterizing groups, using `tl.rank_genes_groups`
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
939 ==================================================================
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
940
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
941 The returned AnnData object contains:
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
942
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
943 - Gene names, ordered according to scores
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
944 - 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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diff changeset
945 - Log2 fold change for each gene for each group, ordered according to scores. It is only provided if method is ‘t-test’ like. This is an approximation calculated from mean-log values.
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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diff changeset
946 - P-values
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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diff changeset
947 - Ajusted p-values
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
948
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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diff changeset
949 This data are stored in the unstructured annotation (uns) and can be accessed using the inspect tool for AnnData objects
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
950
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
951 More details on the `scanpy documentation
5
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diff changeset
952 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.rank_genes_groups.html>`__
0
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diff changeset
953
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
954
1
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
955 Calculate an overlap score between data-deriven marker genes and provided markers (`tl.marker_gene_overlap`)
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
956 ============================================================================================================
0
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diff changeset
957
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
958 Marker gene overlap scores can be quoted as overlap counts, overlap coefficients, or jaccard indices. The method returns a pandas dataframe which can be used to annotate clusters based on marker gene overlaps.
0
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diff changeset
959
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diff changeset
960
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
961 Logarithmize the data matrix (`pp.log1p`)
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
962 =========================================
0
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
963
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
964 More details on the `scanpy documentation
5
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diff changeset
965 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.log1p.html>`__
0
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966
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
967 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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968 ======================================================
0
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
969
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
970 More details on the `scanpy documentation
5
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971 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.scale.html>`__
0
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972
1
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
973 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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974 ====================================================
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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975
a755eaa1cc32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
976 `X = sqrt(X)`
0
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diff changeset
977 ]]></help>
5d2e17328afe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
978 <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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979 </tool>