Mercurial > repos > ebi-gxa > scanpy_find_markers
comparison scanpy-find-markers.xml @ 12:f6291dbb3afc draft
"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> |