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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 ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
author ebi-gxa
date Tue, 27 Feb 2024 16:42:50 +0000
parents f0f78d29130f
children
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31:f0f78d29130f 32:d8f5224005bb
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@+galaxy93" profile="@PROFILE@"> 2 <tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy0" 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"/>
111 <param name="default" value="false"/> 111 <param name="default" value="false"/>
112 <param name="groupby" value="INPUT_OBJ"/> 112 <param name="groupby" value="INPUT_OBJ"/>
113 <param name="key_added" value="GROUPBY_marker"/> 113 <param name="key_added" value="GROUPBY_marker"/>
114 <param name="method" value="t-test_overestim_var"/> 114 <param name="method" value="t-test_overestim_var"/>
115 <param name="rankby_abs" value="false"/> 115 <param name="rankby_abs" value="false"/>
116 <output name="output_h5" file="find_markers.h5" ftype="h5" compare="sim_size"/> 116 <output name="output_h5" ftype="h5">
117 <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/> 117 <assert_contents>
118 <has_h5_keys keys="uns/louvain_1.0_marker"/>
119 </assert_contents>
120 </output>
121 <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size" delta_frac="0.1"/>
118 </test> 122 </test>
119 <test> 123 <test>
120 <param name="input_obj_file" value="louvain_1.0"/> 124 <param name="input_obj_file" value="louvain_1.0"/>
121 <param name="input_format" value="anndata"/> 125 <param name="input_format" value="anndata"/>
122 <param name="output_format" value="no_matrix_output"/> 126 <param name="output_format" value="no_matrix_output"/>
125 <param name="default" value="false"/> 129 <param name="default" value="false"/>
126 <param name="groupby_file" value="groupby.txt"/> 130 <param name="groupby_file" value="groupby.txt"/>
127 <param name="key_added" value="GROUPBY_marker"/> 131 <param name="key_added" value="GROUPBY_marker"/>
128 <param name="method" value="t-test_overestim_var"/> 132 <param name="method" value="t-test_overestim_var"/>
129 <param name="rankby_abs" value="false"/> 133 <param name="rankby_abs" value="false"/>
130 <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/> 134 <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size" delta_frac="0.1"/>
131 </test> 135 </test>
132 <test> 136 <test>
133 <param name="input_obj_file" value="mnn.h5"/> 137 <param name="input_obj_file" value="mnn.h5"/>
134 <param name="input_format" value="anndata"/> 138 <param name="input_format" value="anndata"/>
135 <param name="n_genes" value="50"/> 139 <param name="n_genes" value="50"/>