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comparison scanpy-find-markers.xml @ 12:f6291dbb3afc 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 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
author ebi-gxa
date Mon, 07 Sep 2020 13:05:52 +0000
parents 0d63195a9b9f
children cc776860fae1
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11:af9cf232d6c9 12:f6291dbb3afc
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@+galaxy10" profile="@PROFILE@"> 2 <tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy0" 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"/>
20 #if $settings.groups 20 #if $settings.groups
21 --groups '${settings.groups}' 21 --groups '${settings.groups}'
22 #end if 22 #end if
23 --reference '${settings.reference}' 23 --reference '${settings.reference}'
24 --filter-params 'min_in_group_fraction:${settings.min_in_group_fraction},max_out_group_fraction:${settings.max_out_group_fraction},min_fold_change:${settings.min_fold_change}' 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}'
25 #end if 25 #end if
26 $settings.pts $settings.tie_correct
26 @INPUT_OPTS@ 27 @INPUT_OPTS@
27 @OUTPUT_OPTS@ 28 @OUTPUT_OPTS@
28 ]]></command> 29 ]]></command>
29 30
30 <inputs> 31 <inputs>
53 help="Post-test filtering to only keep genes expressed in at least this fraction of cells in the test group."/> 54 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 <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 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 <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."/> 58 help="Post-test filtering to only keep genes with at least this fold change of expression relative to the reference group."/>
59 <param name="pts" argument="--pts" type="boolean" checked="false" label="Compute the fraction of cells expressing the genes?" truevalue="--pts" falsevalue="" />
60 <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=""/>
58 </when> 61 </when>
59 </conditional> 62 </conditional>
60 </inputs> 63 </inputs>
61 64
62 <outputs> 65 <outputs>