Mercurial > repos > ebi-gxa > scanpy_find_markers

comparison scanpy-find-markers.xml @ 15:cc776860fae1 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 fda35ff3ea8609c4bb5e1fd9e58ba70cd5b5a997-dirty"
author ebi-gxa
date Wed, 30 Sep 2020 11:16:08 +0000
parents f6291dbb3afc
children 1670af5eee46
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14:fb9bd74c32b0 15:cc776860fae1
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@+galaxy1" 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"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '${input_obj_file}' input.h5 && 9 ln -s '${input_obj_file}' input.h5 &&
10 PYTHONIOENCODING=utf-8 scanpy-find-markers 10 PYTHONIOENCODING=utf-8 scanpy-find-markers
11 #if $output_markers 11 #if $output_markers
12 --save output.csv 12 --save diffexp.tsv
13 #end if 13 #end if
14 --n-genes '${n_genes}' 14 --n-genes '${n_genes}'
15 #set groupby = $groupby.replace('INPUT_OBJ', $input_obj_file.__getattr__('name'))
15 --groupby '${groupby}' 16 --groupby '${groupby}'
17 #if $settings.key_added
18 #set key_added = $settings.key_added.replace('GROUPBY', $groupby.__str__)
19 --key-added '${key_added}'
20 #end if
16 #if $settings.default == "false" 21 #if $settings.default == "false"
17 --method '${settings.method}' 22 --method '${settings.method}'
18 ${settings.use_raw} 23 ${settings.use_raw}
19 ${settings.rankby_abs} 24 ${settings.rankby_abs}
20 #if $settings.groups 25 #if $settings.groups
29 ]]></command> 34 ]]></command>
30 35
31 <inputs> 36 <inputs>
32 <expand macro="input_object_params"/> 37 <expand macro="input_object_params"/>
33 <expand macro="output_object_params"/> 38 <expand macro="output_object_params"/>
34 <param name="output_markers" type="boolean" checked="true" label="Output markers table in csv format"/> 39 <param name="output_markers" type="boolean" checked="true" label="Output markers table in tsv format"/>
35 <param name="n_genes" argument="--n-genes" type="integer" value="50" label="Number of top genes to show per group/cluster"/> 40 <param name="n_genes" argument="--n-genes" type="integer" value="50" label="Number of top genes to show per group/cluster"/>
36 <param name="groupby" argument="--groupby" type="text" value="louvain" label="The sample grouping/clustering to use."/> 41 <param name="groupby" argument="--groupby" type="text" value="louvain" label="The sample grouping/clustering to use."/>
37 <conditional name="settings"> 42 <conditional name="settings">
38 <param name="default" type="boolean" checked="true" label="Use programme defaults"/> 43 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
39 <when value="true"/> 44 <when value="true"/>
40 <when value="false"> 45 <when value="false">
46 <param name="key_added" argument="--key-added" type="text" optional="true"
47 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."/>
41 <param name="method" argument="--method" type="select" label="Method for testing differentially expressed genes"> 48 <param name="method" argument="--method" type="select" label="Method for testing differentially expressed genes">
42 <option value="t-test_overestim_var" selected="true">t-test with over-estimated variance</option> 49 <option value="t-test_overestim_var" selected="true">t-test with over-estimated variance</option>
43 <option value="t-test">t-test</option> 50 <option value="t-test">t-test</option>
44 <option value="wilcoxon">wilcoxon test, currently broken don't use</option> 51 <option value="wilcoxon">wilcoxon test, currently broken don't use</option>
45 <option value="logreg">logistic regression</option> 52 <option value="logreg">logistic regression</option>
62 </conditional> 69 </conditional>
63 </inputs> 70 </inputs>
64 71
65 <outputs> 72 <outputs>
66 <expand macro="output_data_obj" description="Marker genes"/> 73 <expand macro="output_data_obj" description="Marker genes"/>
67 <data name="output_csv" format="csv" from_work_dir="output.csv" label="${tool.name} on ${on_string}: Marker table"> 74 <data name="output_tsv" format="tabular" from_work_dir="diffexp.tsv" label="${tool.name} on ${on_string}: Marker table">
68 <filter>output_markers</filter> 75 <filter>output_markers</filter>
69 </data> 76 </data>
70 </outputs> 77 </outputs>
71 78
72 <tests> 79 <tests>
73 <test> 80 <test>
74 <param name="input_obj_file" value="find_cluster.h5"/> 81 <param name="input_obj_file" value="louvain_1.0"/>
75 <param name="input_format" value="anndata"/> 82 <param name="input_format" value="anndata"/>
76 <param name="output_format" value="anndata"/> 83 <param name="output_format" value="anndata"/>
77 <param name="output_csv" value="true"/> 84 <param name="output_tsv" value="true"/>
78 <param name="n_genes" value="50"/> 85 <param name="n_genes" value="50"/>
79 <param name="output_markers" value="false"/> 86 <param name="output_markers" value="true"/>
80 <param name="default" value="false"/> 87 <param name="default" value="false"/>
81 <param name="groupby" value="louvain"/> 88 <param name="groupby" value="INPUT_OBJ"/>
89 <param name="key_added" value="GROUPBY_marker"/>
82 <param name="method" value="t-test_overestim_var"/> 90 <param name="method" value="t-test_overestim_var"/>
83 <param name="rankby_abs" value="false"/> 91 <param name="rankby_abs" value="false"/>
84 <output name="output_h5" file="find_markers.h5" ftype="h5" compare="sim_size"/> 92 <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"/>
85 </test> 94 </test>
86 </tests> 95 </tests>
87 96
88 <help><![CDATA[ 97 <help><![CDATA[
89 ============================================================= 98 =============================================================