Mercurial > repos > ebi-gxa > scanpy_find_markers

comparison scanpy-find-markers.xml @ 30:64259337506f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit d01fa18235ac692874cd3cfddef33696c2df8ac1-dirty
author ebi-gxa
date Sat, 15 Jul 2023 08:44:51 +0000
parents 81c34e67f262
children f0f78d29130f
comparison
equal deleted inserted replaced
29:81c34e67f262 30:64259337506f
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@"> 2 <tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy91" profile="@PROFILE@">
3 <description>to find differentially expressed genes between groups</description> 3 <description>to find differentially expressed genes between groups</description>
4 <macros> 4 <macros>
5 <import>scanpy_macros2.xml</import> 5 <import>scanpy_macros2.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
24 #if $settings.key_added 24 #if $settings.key_added
25 #set key_added = $settings.key_added.replace('GROUPBY', $groupby.__str__) 25 #set key_added = $settings.key_added.replace('GROUPBY', $groupby.__str__)
26 --key-added '${key_added}' 26 --key-added '${key_added}'
27 #end if 27 #end if
28 --method '${settings.method}' 28 --method '${settings.method}'
29 ${settings.use_raw}
30 ${settings.rankby_abs} 29 ${settings.rankby_abs}
31 #if $settings.groups 30 #if $settings.groups
32 --groups '${settings.groups}' 31 --groups '${settings.groups}'
33 #end if 32 #end if
34 --reference '${settings.reference}' 33 --reference '${settings.reference}'
35 #if $settings.filter.default == "false" 34 #if $settings.filter.default == "false"
36 --filter-params 'min_in_group_fraction:${settings.filter.min_in_group_fraction},max_out_group_fraction:${settings.filter.max_out_group_fraction},min_fold_change:${settings.filter.min_fold_change}' 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}'
36 #end if
37 #if $settings.layer
38 --layer '${settings.layer}'
39 --no-raw
40 #else
41 ${settings.use_raw}
37 #end if 42 #end if
38 $settings.pts $settings.tie_correct 43 $settings.pts $settings.tie_correct
39 #end if 44 #end if
40 @INPUT_OPTS@ 45 @INPUT_OPTS@
41 @OUTPUT_OPTS@ 46 @OUTPUT_OPTS@
56 <param name="key_added" argument="--key-added" type="text" optional="true" 61 <param name="key_added" argument="--key-added" type="text" optional="true"
57 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."/> 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."/>
58 <param name="method" argument="--method" type="select" label="Method for testing differentially expressed genes"> 63 <param name="method" argument="--method" type="select" label="Method for testing differentially expressed genes">
59 <option value="t-test_overestim_var" selected="true">t-test with over-estimated variance</option> 64 <option value="t-test_overestim_var" selected="true">t-test with over-estimated variance</option>
60 <option value="t-test">t-test</option> 65 <option value="t-test">t-test</option>
61 <option value="wilcoxon">wilcoxon test, currently broken don't use</option> 66 <option value="wilcoxon">wilcoxon test</option>
62 <option value="logreg">logistic regression</option> 67 <option value="logreg">logistic regression</option>
63 </param> 68 </param>
64 <param name="use_raw" type="boolean" truevalue="--use-raw" falsevalue="--no-raw" checked="true" 69 <param name="use_raw" type="boolean" truevalue="--use-raw" falsevalue="--no-raw" checked="true"
65 label="Use raw attribute if present"/> 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)."/>
66 <param name="rankby_abs" argument="--rankby_abs" type="boolean" truevalue="--rankby-abs" falsevalue="" checked="false" 71 <param name="rankby_abs" argument="--rankby_abs" type="boolean" truevalue="--rankby-abs" falsevalue="" checked="false"
67 label="Rank by absolute value of the scores instead of the scores"/> 72 label="Rank by absolute value of the scores instead of the scores"/>
68 <param name="groups" argument="--groups" optional="true" type="text" label="Subset of groups/clusters to which comparisons shell be restricted."/> 73 <param name="groups" argument="--groups" optional="true" type="text"
74 label="Subset of groups/clusters to which comparisons should be restricted"
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."/>
69 <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"/> 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"/>
70 <conditional name="filter"> 77 <conditional name="filter">
71 <param name="default" type="boolean" checked="false" label="Use filtering defaults"/> 78 <param name="default" type="boolean" checked="false" label="Use filtering defaults"/>
72 <when value="true"/> 79 <when value="true"/>
73 <when value="false"> 80 <when value="false">
77 help="Post-test filtering to only keep genes expressed in at most this fraction of cells in the reference group."/> 84 help="Post-test filtering to only keep genes expressed in at most this fraction of cells in the reference group."/>
78 <param name="min_fold_change" type="float" value="2" label="Minimum fold change" 85 <param name="min_fold_change" type="float" value="2" label="Minimum fold change"
79 help="Post-test filtering to only keep genes with at least this fold change of expression relative to the reference group."/> 86 help="Post-test filtering to only keep genes with at least this fold change of expression relative to the reference group."/>
80 </when> 87 </when>
81 </conditional> 88 </conditional>
89 <param name="layer" argument="--layer" type="text" optional="true" label="Layer to use for marker genes computation"
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."/>
82 <param name="pts" argument="--pts" type="boolean" checked="false" label="Compute the fraction of cells expressing the genes?" truevalue="--pts" falsevalue="" /> 91 <param name="pts" argument="--pts" type="boolean" checked="false" label="Compute the fraction of cells expressing the genes?" truevalue="--pts" falsevalue="" />
83 <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=""/> 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=""/>
84 </when> 93 </when>
85 </conditional> 94 </conditional>
86 </inputs> 95 </inputs>
118 <param name="key_added" value="GROUPBY_marker"/> 127 <param name="key_added" value="GROUPBY_marker"/>
119 <param name="method" value="t-test_overestim_var"/> 128 <param name="method" value="t-test_overestim_var"/>
120 <param name="rankby_abs" value="false"/> 129 <param name="rankby_abs" value="false"/>
121 <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/> 130 <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/>
122 </test> 131 </test>
132 <test>
133 <param name="input_obj_file" value="mnn.h5"/>
134 <param name="input_format" value="anndata"/>
135 <param name="n_genes" value="50"/>
136 <param name="output_markers" value="true"/>
137 <param name="default" value="false"/>
138 <param name="groupby" value="louvain"/>
139 <param name="key_added" value="l_markers"/>
140 <param name="method" value="wilcoxon"/>
141 <param name="layer" value="mnn"/>
142 <output name="output_h5ad" ftype="h5ad">
143 <assert_contents>
144 <has_h5_keys keys="uns/l_markers_mnn"/>
145 </assert_contents>
146 </output>
147 </test>
123 </tests> 148 </tests>
124 149
125 <help><![CDATA[ 150 <help><![CDATA[
126 ============================================================= 151 =============================================================
127 Rank genes for characterizing groups (`tl.rank_genes_groups`) 152 Rank genes for characterizing groups (`tl.rank_genes_groups`)