Mercurial > repos > ebi-gxa > scanpy_find_markers

annotate scanpy-find-markers.xml @ 31:f0f78d29130f draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 162313dc6ba68efc5003b1bd9b71a40aec87d826-dirty
author ebi-gxa
date Fri, 13 Oct 2023 14:07:40 +0000
parents 64259337506f
children d8f5224005bb
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c608fd80ec15 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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1 <?xml version="1.0" encoding="utf-8"?>
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f0f78d29130f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 162313dc6ba68efc5003b1bd9b71a40aec87d826-dirty
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2 <tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
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c608fd80ec15 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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3 <description>to find differentially expressed genes between groups</description>
c608fd80ec15 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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4 <macros>
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5 <import>scanpy_macros2.xml</import>
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c608fd80ec15 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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6 </macros>
c608fd80ec15 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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7 <expand macro="requirements"/>
c608fd80ec15 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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8 <command detect_errors="exit_code"><![CDATA[
c608fd80ec15 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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9 ln -s '${input_obj_file}' input.h5 &&
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10 PYTHONIOENCODING=utf-8 scanpy-find-markers
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11 #if $output_markers
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12 --save diffexp.tsv
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13 #end if
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14 --n-genes '${n_genes}'
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15 #if $groupby_file
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16 #set f = open($groupby_file.__str__)
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17 #set groupby = f.read().strip()
f04dd4e5b6a7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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18 #silent f.close
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19 #else
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20 #set groupby = $groupby.replace('INPUT_OBJ', $input_obj_file.__getattr__('name'))
f04dd4e5b6a7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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21 #end if
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22 --groupby '${groupby}'
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23 #if $settings.default == "false"
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24 #if $settings.key_added
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25 #set key_added = $settings.key_added.replace('GROUPBY', $groupby.__str__)
1670af5eee46 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 0fc0cc467014e750dbaa6c47b528b25af0bdc0c4-dirty"
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26 --key-added '${key_added}'
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27 #end if
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28 --method '${settings.method}'
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29 ${settings.rankby_abs}
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30 #if $settings.groups
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31 --groups '${settings.groups}'
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32 #end if
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33 --reference '${settings.reference}'
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34 #if $settings.filter.default == "false"
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35 --filter-params 'min_in_group_fraction:${settings.filter.min_in_group_fraction},max_out_group_fraction:${settings.filter.max_out_group_fraction},min_fold_change:${settings.filter.min_fold_change}'
a57c0538e56b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8724e7a15bd07ee890908acc22efb826052f2ef6-dirty"
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36 #end if
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37 #if $settings.layer
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38 --layer '${settings.layer}'
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39 --no-raw
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40 #else
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41 ${settings.use_raw}
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42 #end if
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43 $settings.pts $settings.tie_correct
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44 #end if
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45 @INPUT_OPTS@
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46 @OUTPUT_OPTS@
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47 ]]></command>
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48
c608fd80ec15 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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49 <inputs>
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50 <expand macro="input_object_params"/>
c608fd80ec15 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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51 <expand macro="output_object_params"/>
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52 <param name="output_markers" type="boolean" checked="true" label="Output markers table in tsv format"/>
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c608fd80ec15 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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53 <param name="n_genes" argument="--n-genes" type="integer" value="50" label="Number of top genes to show per group/cluster"/>
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54 <param name="groupby" argument="--groupby" type="text" value="louvain" label="The sample grouping/clustering to use."/>
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55 <param name="groupby_file" argument="--groupby" type="data" format="txt,tsv" optional="true"
f04dd4e5b6a7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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56 label="File with groupby. Overrides the groupby setting"/>
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57 <conditional name="settings">
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58 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
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59 <when value="true"/>
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60 <when value="false">
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61 <param name="key_added" argument="--key-added" type="text" optional="true"
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62 label="The key in adata.uns information is saved to. If included, the keyword 'GROUPBY' will be substituted with the value of the groupby setting."/>
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63 <param name="method" argument="--method" type="select" label="Method for testing differentially expressed genes">
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64 <option value="t-test_overestim_var" selected="true">t-test with over-estimated variance</option>
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65 <option value="t-test">t-test</option>
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66 <option value="wilcoxon">wilcoxon test</option>
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67 <option value="logreg">logistic regression</option>
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68 </param>
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69 <param name="use_raw" type="boolean" truevalue="--use-raw" falsevalue="--no-raw" checked="true"
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70 label="Use raw attribute if present" help="Uses adata.raw, usually what was available before processing. If the layer option is set, this will be ignored (raw will not be used)."/>
1
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71 <param name="rankby_abs" argument="--rankby_abs" type="boolean" truevalue="--rankby-abs" falsevalue="" checked="false"
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72 label="Rank by absolute value of the scores instead of the scores"/>
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73 <param name="groups" argument="--groups" optional="true" type="text"
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74 label="Subset of groups/clusters to which comparisons should be restricted"
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75 help="Comma separated list of groups existing within the groupby field in obs. Currently it fails if a single group is given, provide at least two."/>
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76 <param name="reference" argument="--reference" type="text" value="rest" label="If 'rest', compare to the union of the rest of the group/cluster. If a group identifier, compare to that group"/>
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77 <conditional name="filter">
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78 <param name="default" type="boolean" checked="false" label="Use filtering defaults"/>
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79 <when value="true"/>
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80 <when value="false">
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81 <param name="min_in_group_fraction" type="float" min="0.0" max="1.0" value="0.25" label="Minimum in-group fraction"
a57c0538e56b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8724e7a15bd07ee890908acc22efb826052f2ef6-dirty"
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82 help="Post-test filtering to only keep genes expressed in at least this fraction of cells in the test group."/>
a57c0538e56b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8724e7a15bd07ee890908acc22efb826052f2ef6-dirty"
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83 <param name="max_out_group_fraction" type="float" min="0.0" max="1.0" value="0.5" label="Maximum out-group fraction"
a57c0538e56b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8724e7a15bd07ee890908acc22efb826052f2ef6-dirty"
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84 help="Post-test filtering to only keep genes expressed in at most this fraction of cells in the reference group."/>
a57c0538e56b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8724e7a15bd07ee890908acc22efb826052f2ef6-dirty"
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85 <param name="min_fold_change" type="float" value="2" label="Minimum fold change"
a57c0538e56b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8724e7a15bd07ee890908acc22efb826052f2ef6-dirty"
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86 help="Post-test filtering to only keep genes with at least this fold change of expression relative to the reference group."/>
a57c0538e56b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8724e7a15bd07ee890908acc22efb826052f2ef6-dirty"
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87 </when>
a57c0538e56b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8724e7a15bd07ee890908acc22efb826052f2ef6-dirty"
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88 </conditional>
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89 <param name="layer" argument="--layer" type="text" optional="true" label="Layer to use for marker genes computation"
64259337506f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit d01fa18235ac692874cd3cfddef33696c2df8ac1-dirty
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90 help="The method prefers matrices/layers that are logged. Leave empty to use the default .X matrix. It will override the use of raw if set."/>
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91 <param name="pts" argument="--pts" type="boolean" checked="false" label="Compute the fraction of cells expressing the genes?" truevalue="--pts" falsevalue="" />
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92 <param name="tie_correct" argument="--tie-correct" type="boolean" checked="false" label="Use tie correction for 'wilcoxon' scores. Used only for 'wilcoxon'." truevalue="--tie-correct" falsevalue=""/>
0
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93 </when>
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94 </conditional>
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95 </inputs>
c608fd80ec15 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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96
c608fd80ec15 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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97 <outputs>
5
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98 <expand macro="output_data_obj" description="Marker genes"/>
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99 <data name="output_tsv" format="tabular" from_work_dir="diffexp.tsv" label="${tool.name} on ${on_string}: Marker table">
0
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100 <filter>output_markers</filter>
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101 </data>
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102 </outputs>
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103
c608fd80ec15 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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104 <tests>
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105 <test>
15
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106 <param name="input_obj_file" value="louvain_1.0"/>
0
c608fd80ec15 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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107 <param name="input_format" value="anndata"/>
c608fd80ec15 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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108 <param name="output_format" value="anndata"/>
c608fd80ec15 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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109 <param name="n_genes" value="50"/>
15
cc776860fae1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit fda35ff3ea8609c4bb5e1fd9e58ba70cd5b5a997-dirty"
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110 <param name="output_markers" value="true"/>
0
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111 <param name="default" value="false"/>
15
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112 <param name="groupby" value="INPUT_OBJ"/>
cc776860fae1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit fda35ff3ea8609c4bb5e1fd9e58ba70cd5b5a997-dirty"
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113 <param name="key_added" value="GROUPBY_marker"/>
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114 <param name="method" value="t-test_overestim_var"/>
c608fd80ec15 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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115 <param name="rankby_abs" value="false"/>
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116 <output name="output_h5" file="find_markers.h5" ftype="h5" compare="sim_size"/>
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117 <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/>
0
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118 </test>
17
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119 <test>
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120 <param name="input_obj_file" value="louvain_1.0"/>
f04dd4e5b6a7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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121 <param name="input_format" value="anndata"/>
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81c34e67f262 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6c9d530aa653101e9e21804393ec11f38cddf027-dirty
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122 <param name="output_format" value="no_matrix_output"/>
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f04dd4e5b6a7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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123 <param name="n_genes" value="50"/>
f04dd4e5b6a7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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124 <param name="output_markers" value="true"/>
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125 <param name="default" value="false"/>
f04dd4e5b6a7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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126 <param name="groupby_file" value="groupby.txt"/>
f04dd4e5b6a7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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127 <param name="key_added" value="GROUPBY_marker"/>
f04dd4e5b6a7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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128 <param name="method" value="t-test_overestim_var"/>
f04dd4e5b6a7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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129 <param name="rankby_abs" value="false"/>
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130 <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/>
f04dd4e5b6a7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"
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131 </test>
30
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132 <test>
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133 <param name="input_obj_file" value="mnn.h5"/>
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134 <param name="input_format" value="anndata"/>
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135 <param name="n_genes" value="50"/>
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136 <param name="output_markers" value="true"/>
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137 <param name="default" value="false"/>
64259337506f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit d01fa18235ac692874cd3cfddef33696c2df8ac1-dirty
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138 <param name="groupby" value="louvain"/>
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139 <param name="key_added" value="l_markers"/>
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140 <param name="method" value="wilcoxon"/>
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141 <param name="layer" value="mnn"/>
64259337506f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit d01fa18235ac692874cd3cfddef33696c2df8ac1-dirty
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142 <output name="output_h5ad" ftype="h5ad">
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143 <assert_contents>
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144 <has_h5_keys keys="uns/l_markers_mnn"/>
64259337506f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit d01fa18235ac692874cd3cfddef33696c2df8ac1-dirty
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145 </assert_contents>
64259337506f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit d01fa18235ac692874cd3cfddef33696c2df8ac1-dirty
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146 </output>
64259337506f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit d01fa18235ac692874cd3cfddef33696c2df8ac1-dirty
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147 </test>
0
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148 </tests>
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149
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150 <help><![CDATA[
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151 =============================================================
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152 Rank genes for characterizing groups (`tl.rank_genes_groups`)
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153 =============================================================
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154
c608fd80ec15 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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155 Rank genes for characterizing groups.
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156
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157 @HELP@
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158
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159 @VERSION_HISTORY@
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160 ]]></help>
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161 <expand macro="citations"/>
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162 </tool>