Mercurial > repos > ebi-gxa > scanpy_find_markers

comparison scanpy-find-markers.xml @ 1:71668dd2d47b 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 4846776f55931e176f7e77af7c185ec6fec7d142"
author ebi-gxa
date Mon, 16 Sep 2019 08:12:48 -0400
parents c608fd80ec15
children 74100c9351bc
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0:c608fd80ec15 1:71668dd2d47b
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@+galaxy1"> 2 <tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy1">
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_macros.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.py 10 PYTHONIOENCODING=utf-8 scanpy-find-markers
11 -i input.h5 11 #if $output_markers
12 -f '${input_format}' 12 --save output.csv
13 -o output.h5 13 #end if
14 -F '${output_format}' 14 --n-genes '${n_genes}'
15 -n '${n_genes}' 15 --groupby '${groupby}'
16 #if $output_markers 16 #if $settings.default == "false"
17 --output-text-file output.csv 17 --method '${settings.method}'
18 ${settings.use_raw}
19 ${settings.rankby_abs}
20 #if $settings.groups
21 --groups '${settings.groups}'
18 #end if 22 #end if
19 #if $settings.default == "false" 23 --reference '${settings.reference}'
20 -g '${settings.groupby}' 24 --filter-params 'min_in_group_fraction:${settings.min_in_group_fraction},max_out_group_fraction:${settings.max_out_group_fraction},min_fold_change:${settings.min_fold_change}'
21 --reference '${settings.reference}'
22 --method '${settings.method}'
23 #if $settings.use_raw == "false"
24 --no-raw
25 #end if
26 #if $settings.rankby_abs
27 --rankby_abs
28 #end if
29 #if $settings.groups
30 --groups '${settings.groups}'
31 #end if
32 #end if 25 #end if
26 @INPUT_OPTS@
27 @OUTPUT_OPTS@
33 ]]></command> 28 ]]></command>
34 29
35 <inputs> 30 <inputs>
36 <expand macro="input_object_params"/> 31 <expand macro="input_object_params"/>
37 <expand macro="output_object_params"/> 32 <expand macro="output_object_params"/>
33 <param name="output_markers" type="boolean" checked="true" label="Output markers table in csv format"/>
38 <param name="n_genes" argument="--n-genes" type="integer" value="50" label="Number of top genes to show per group/cluster"/> 34 <param name="n_genes" argument="--n-genes" type="integer" value="50" label="Number of top genes to show per group/cluster"/>
39 <param name="output_markers" type="boolean" checked="true" label="Output markers table in csv format"/> 35 <param name="groupby" argument="--groupby" type="text" value="louvain" label="The sample grouping/clustering to use."/>
40 <conditional name="settings"> 36 <conditional name="settings">
41 <param name="default" type="boolean" checked="true" label="Use programme defaults"/> 37 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
42 <when value="true"/> 38 <when value="true"/>
43 <when value="false"> 39 <when value="false">
44 <param name="groupby" argument="--groupby" type="text" value="louvain" label="The sample grouping/clustering to use."/>
45 <param name="use_raw" type="boolean" checked="true" label="Use raw attribute if present"/>
46 <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"/>
47 <param name="method" argument="--method" type="select" label="Method for testing differentially expressed genes"> 40 <param name="method" argument="--method" type="select" label="Method for testing differentially expressed genes">
48 <option value="t-test_overestim_var" selected="true">t-test with over-estimated variance</option> 41 <option value="t-test_overestim_var" selected="true">t-test with over-estimated variance</option>
49 <option value="t-test">t-test</option> 42 <option value="t-test">t-test</option>
50 <option value="wilcoxon">wilcoxon test, currently broken don't use</option> 43 <option value="wilcoxon">wilcoxon test, currently broken don't use</option>
51 <option value="logreg">logistic regression</option> 44 <option value="logreg">logistic regression</option>
52 </param> 45 </param>
53 <param name="rankby_abs" argument="--rankby_abs" type="boolean" checked="false" label="Rank by absolute value of the scores instead of the scores"/> 46 <param name="use_raw" type="boolean" truevalue="--use-raw" falsevalue="--no-raw" checked="true"
47 label="Use raw attribute if present"/>
48 <param name="rankby_abs" argument="--rankby_abs" type="boolean" truevalue="--rankby-abs" falsevalue="" checked="false"
49 label="Rank by absolute value of the scores instead of the scores"/>
54 <param name="groups" argument="--groups" optional="true" type="text" label="Subset of groups/clusters to which comparisons shell be restricted."/> 50 <param name="groups" argument="--groups" optional="true" type="text" label="Subset of groups/clusters to which comparisons shell be restricted."/>
51 <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"/>
52 <param name="min_in_group_fraction" type="float" min="0.0" max="1.0" value="0.25" label="Minimum in-group fraction"
53 help="Post-test filtering to only keep genes expressed in at least this fraction of cells in the test group."/>
54 <param name="max_out_group_fraction" type="float" min="0.0" max="1.0" value="0.5" label="Maximum out-group fraction"
55 help="Post-test filtering to only keep genes expressed in at most this fraction of cells in the reference group."/>
56 <param name="min_fold_change" type="float" value="2" label="Minimum fold change"
57 help="Post-test filtering to only keep genes with at least this fold change of expression relative to the reference group."/>
55 </when> 58 </when>
56 </conditional> 59 </conditional>
57 </inputs> 60 </inputs>
58 61
59 <outputs> 62 <outputs>