Mercurial > repos > ebi-gxa > scanpy_find_markers

comparison scanpy-find-markers.xml @ 29:81c34e67f262 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 6c9d530aa653101e9e21804393ec11f38cddf027-dirty
author ebi-gxa
date Thu, 16 Feb 2023 13:28:49 +0000
parents eb01a7e59e9a
children 64259337506f
comparison
equal deleted inserted replaced
28:eb01a7e59e9a 29:81c34e67f262
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@+galaxy0" profile="@PROFILE@"> 2 <tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy9" 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"/>
95 <tests> 95 <tests>
96 <test> 96 <test>
97 <param name="input_obj_file" value="louvain_1.0"/> 97 <param name="input_obj_file" value="louvain_1.0"/>
98 <param name="input_format" value="anndata"/> 98 <param name="input_format" value="anndata"/>
99 <param name="output_format" value="anndata"/> 99 <param name="output_format" value="anndata"/>
100 <param name="output_tsv" value="true"/>
101 <param name="n_genes" value="50"/> 100 <param name="n_genes" value="50"/>
102 <param name="output_markers" value="true"/> 101 <param name="output_markers" value="true"/>
103 <param name="default" value="false"/> 102 <param name="default" value="false"/>
104 <param name="groupby" value="INPUT_OBJ"/> 103 <param name="groupby" value="INPUT_OBJ"/>
105 <param name="key_added" value="GROUPBY_marker"/> 104 <param name="key_added" value="GROUPBY_marker"/>
109 <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/> 108 <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/>
110 </test> 109 </test>
111 <test> 110 <test>
112 <param name="input_obj_file" value="louvain_1.0"/> 111 <param name="input_obj_file" value="louvain_1.0"/>
113 <param name="input_format" value="anndata"/> 112 <param name="input_format" value="anndata"/>
114 <param name="output_format" value="anndata"/> 113 <param name="output_format" value="no_matrix_output"/>
115 <param name="output_tsv" value="true"/>
116 <param name="n_genes" value="50"/> 114 <param name="n_genes" value="50"/>
117 <param name="output_markers" value="true"/> 115 <param name="output_markers" value="true"/>
118 <param name="default" value="false"/> 116 <param name="default" value="false"/>
119 <param name="groupby_file" value="groupby.txt"/> 117 <param name="groupby_file" value="groupby.txt"/>
120 <param name="key_added" value="GROUPBY_marker"/> 118 <param name="key_added" value="GROUPBY_marker"/>
121 <param name="method" value="t-test_overestim_var"/> 119 <param name="method" value="t-test_overestim_var"/>
122 <param name="rankby_abs" value="false"/> 120 <param name="rankby_abs" value="false"/>
123 <output name="output_h5" file="find_markers.h5" ftype="h5" compare="sim_size"/>
124 <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/> 121 <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/>
125 </test> 122 </test>
126 </tests> 123 </tests>
127 124
128 <help><![CDATA[ 125 <help><![CDATA[