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comparison scanpy-find-markers.xml @ 17:f04dd4e5b6a7 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 a49eda957d6c894fee1514c9df649444966691ce-dirty"
author ebi-gxa
date Thu, 15 Oct 2020 16:06:41 +0000
parents 1670af5eee46
children bfdca1eb4548
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16:1670af5eee46 17:f04dd4e5b6a7
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@+galaxy2" profile="@PROFILE@"> 2 <tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy3" 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"/>
10 PYTHONIOENCODING=utf-8 scanpy-find-markers 10 PYTHONIOENCODING=utf-8 scanpy-find-markers
11 #if $output_markers 11 #if $output_markers
12 --save diffexp.tsv 12 --save diffexp.tsv
13 #end if 13 #end if
14 --n-genes '${n_genes}' 14 --n-genes '${n_genes}'
15 #set groupby = $groupby.replace('INPUT_OBJ', $input_obj_file.__getattr__('name')) 15 #if $groupby_file
16 #set f = open($groupby_file.__str__)
17 #set groupby = f.read().strip()
18 #silent f.close
19 #else
20 #set groupby = $groupby.replace('INPUT_OBJ', $input_obj_file.__getattr__('name'))
21 #end if
16 --groupby '${groupby}' 22 --groupby '${groupby}'
17 #if $settings.default == "false" 23 #if $settings.default == "false"
18 #if $settings.key_added 24 #if $settings.key_added
19 #set key_added = $settings.key_added.replace('GROUPBY', $groupby.__str__) 25 #set key_added = $settings.key_added.replace('GROUPBY', $groupby.__str__)
20 --key-added '${key_added}' 26 --key-added '${key_added}'
37 <expand macro="input_object_params"/> 43 <expand macro="input_object_params"/>
38 <expand macro="output_object_params"/> 44 <expand macro="output_object_params"/>
39 <param name="output_markers" type="boolean" checked="true" label="Output markers table in tsv format"/> 45 <param name="output_markers" type="boolean" checked="true" label="Output markers table in tsv format"/>
40 <param name="n_genes" argument="--n-genes" type="integer" value="50" label="Number of top genes to show per group/cluster"/> 46 <param name="n_genes" argument="--n-genes" type="integer" value="50" label="Number of top genes to show per group/cluster"/>
41 <param name="groupby" argument="--groupby" type="text" value="louvain" label="The sample grouping/clustering to use."/> 47 <param name="groupby" argument="--groupby" type="text" value="louvain" label="The sample grouping/clustering to use."/>
48 <param name="groupby_file" argument="--groupby" type="data" format="txt,tsv" optional="true"
49 label="File with groupby. Overrides the groupby setting"/>
42 <conditional name="settings"> 50 <conditional name="settings">
43 <param name="default" type="boolean" checked="true" label="Use programme defaults"/> 51 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
44 <when value="true"/> 52 <when value="true"/>
45 <when value="false"> 53 <when value="false">
46 <param name="key_added" argument="--key-added" type="text" optional="true" 54 <param name="key_added" argument="--key-added" type="text" optional="true"
90 <param name="method" value="t-test_overestim_var"/> 98 <param name="method" value="t-test_overestim_var"/>
91 <param name="rankby_abs" value="false"/> 99 <param name="rankby_abs" value="false"/>
92 <output name="output_h5" file="find_markers.h5" ftype="h5" compare="sim_size"/> 100 <output name="output_h5" file="find_markers.h5" ftype="h5" compare="sim_size"/>
93 <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/> 101 <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/>
94 </test> 102 </test>
103 <test>
104 <param name="input_obj_file" value="louvain_1.0"/>
105 <param name="input_format" value="anndata"/>
106 <param name="output_format" value="anndata"/>
107 <param name="output_tsv" value="true"/>
108 <param name="n_genes" value="50"/>
109 <param name="output_markers" value="true"/>
110 <param name="default" value="false"/>
111 <param name="groupby_file" value="groupby.txt"/>
112 <param name="key_added" value="GROUPBY_marker"/>
113 <param name="method" value="t-test_overestim_var"/>
114 <param name="rankby_abs" value="false"/>
115 <output name="output_h5" file="find_markers.h5" ftype="h5" compare="sim_size"/>
116 <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/>
117 </test>
95 </tests> 118 </tests>
96 119
97 <help><![CDATA[ 120 <help><![CDATA[
98 ============================================================= 121 =============================================================
99 Rank genes for characterizing groups (`tl.rank_genes_groups`) 122 Rank genes for characterizing groups (`tl.rank_genes_groups`)