Mercurial > repos > ebi-gxa > scanpy_find_markers
comparison scanpy-find-markers.xml @ 26:a57c0538e56b draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8724e7a15bd07ee890908acc22efb826052f2ef6-dirty"
author | ebi-gxa |
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date | Wed, 06 Oct 2021 13:10:14 +0000 |
parents | a6a896082cd7 |
children | eb01a7e59e9a |
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25:e2f004c3b2b3 | 26:a57c0538e56b |
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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"/> |
30 ${settings.rankby_abs} | 30 ${settings.rankby_abs} |
31 #if $settings.groups | 31 #if $settings.groups |
32 --groups '${settings.groups}' | 32 --groups '${settings.groups}' |
33 #end if | 33 #end if |
34 --reference '${settings.reference}' | 34 --reference '${settings.reference}' |
35 --filter-params 'min_in_group_fraction:${settings.min_in_group_fraction},max_out_group_fraction:${settings.max_out_group_fraction},min_fold_change:${settings.min_fold_change}' | 35 #if $settings.filter.default == "false" |
36 --filter-params 'min_in_group_fraction:${settings.filter.min_in_group_fraction},max_out_group_fraction:${settings.filter.max_out_group_fraction},min_fold_change:${settings.filter.min_fold_change}' | |
37 #end if | |
36 $settings.pts $settings.tie_correct | 38 $settings.pts $settings.tie_correct |
37 #end if | 39 #end if |
38 @INPUT_OPTS@ | 40 @INPUT_OPTS@ |
39 @OUTPUT_OPTS@ | 41 @OUTPUT_OPTS@ |
40 ]]></command> | 42 ]]></command> |
63 label="Use raw attribute if present"/> | 65 label="Use raw attribute if present"/> |
64 <param name="rankby_abs" argument="--rankby_abs" type="boolean" truevalue="--rankby-abs" falsevalue="" checked="false" | 66 <param name="rankby_abs" argument="--rankby_abs" type="boolean" truevalue="--rankby-abs" falsevalue="" checked="false" |
65 label="Rank by absolute value of the scores instead of the scores"/> | 67 label="Rank by absolute value of the scores instead of the scores"/> |
66 <param name="groups" argument="--groups" optional="true" type="text" label="Subset of groups/clusters to which comparisons shell be restricted."/> | 68 <param name="groups" argument="--groups" optional="true" type="text" label="Subset of groups/clusters to which comparisons shell be restricted."/> |
67 <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"/> | 69 <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"/> |
68 <param name="min_in_group_fraction" type="float" min="0.0" max="1.0" value="0.25" label="Minimum in-group fraction" | 70 <conditional name="filter"> |
69 help="Post-test filtering to only keep genes expressed in at least this fraction of cells in the test group."/> | 71 <param name="default" type="boolean" checked="false" label="Use filtering defaults"/> |
70 <param name="max_out_group_fraction" type="float" min="0.0" max="1.0" value="0.5" label="Maximum out-group fraction" | 72 <when value="true"/> |
71 help="Post-test filtering to only keep genes expressed in at most this fraction of cells in the reference group."/> | 73 <when value="false"> |
72 <param name="min_fold_change" type="float" value="2" label="Minimum fold change" | 74 <param name="min_in_group_fraction" type="float" min="0.0" max="1.0" value="0.25" label="Minimum in-group fraction" |
73 help="Post-test filtering to only keep genes with at least this fold change of expression relative to the reference group."/> | 75 help="Post-test filtering to only keep genes expressed in at least this fraction of cells in the test group."/> |
76 <param name="max_out_group_fraction" type="float" min="0.0" max="1.0" value="0.5" label="Maximum out-group fraction" | |
77 help="Post-test filtering to only keep genes expressed in at most this fraction of cells in the reference group."/> | |
78 <param name="min_fold_change" type="float" value="2" label="Minimum fold change" | |
79 help="Post-test filtering to only keep genes with at least this fold change of expression relative to the reference group."/> | |
80 </when> | |
81 </conditional> | |
74 <param name="pts" argument="--pts" type="boolean" checked="false" label="Compute the fraction of cells expressing the genes?" truevalue="--pts" falsevalue="" /> | 82 <param name="pts" argument="--pts" type="boolean" checked="false" label="Compute the fraction of cells expressing the genes?" truevalue="--pts" falsevalue="" /> |
75 <param name="tie_correct" argument="--tie-correct" type="boolean" checked="false" label="Use tie correction for 'wilcoxon' scores. Used only for 'wilcoxon'." truevalue="--tie-correct" falsevalue=""/> | 83 <param name="tie_correct" argument="--tie-correct" type="boolean" checked="false" label="Use tie correction for 'wilcoxon' scores. Used only for 'wilcoxon'." truevalue="--tie-correct" falsevalue=""/> |
76 </when> | 84 </when> |
77 </conditional> | 85 </conditional> |
78 </inputs> | 86 </inputs> |