| Previous changeset 25:e2f004c3b2b3 (2021-09-28) Next changeset 27:0fc4e76c5c0d (2021-10-15) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8724e7a15bd07ee890908acc22efb826052f2ef6-dirty" |
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modified:
scanpy-find-markers.xml |
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| diff -r e2f004c3b2b3 -r a57c0538e56b scanpy-find-markers.xml --- a/scanpy-find-markers.xml Tue Sep 28 17:44:18 2021 +0000 +++ b/scanpy-find-markers.xml Wed Oct 06 13:10:14 2021 +0000 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> +<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>to find differentially expressed genes between groups</description> <macros> <import>scanpy_macros2.xml</import> @@ -32,7 +32,9 @@ --groups '${settings.groups}' #end if --reference '${settings.reference}' - --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}' + #if $settings.filter.default == "false" + --filter-params 'min_in_group_fraction:${settings.filter.min_in_group_fraction},max_out_group_fraction:${settings.filter.max_out_group_fraction},min_fold_change:${settings.filter.min_fold_change}' + #end if $settings.pts $settings.tie_correct #end if @INPUT_OPTS@ @@ -65,12 +67,18 @@ label="Rank by absolute value of the scores instead of the scores"/> <param name="groups" argument="--groups" optional="true" type="text" label="Subset of groups/clusters to which comparisons shell be restricted."/> <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"/> - <param name="min_in_group_fraction" type="float" min="0.0" max="1.0" value="0.25" label="Minimum in-group fraction" - help="Post-test filtering to only keep genes expressed in at least this fraction of cells in the test group."/> - <param name="max_out_group_fraction" type="float" min="0.0" max="1.0" value="0.5" label="Maximum out-group fraction" - help="Post-test filtering to only keep genes expressed in at most this fraction of cells in the reference group."/> - <param name="min_fold_change" type="float" value="2" label="Minimum fold change" - help="Post-test filtering to only keep genes with at least this fold change of expression relative to the reference group."/> + <conditional name="filter"> + <param name="default" type="boolean" checked="false" label="Use filtering defaults"/> + <when value="true"/> + <when value="false"> + <param name="min_in_group_fraction" type="float" min="0.0" max="1.0" value="0.25" label="Minimum in-group fraction" + help="Post-test filtering to only keep genes expressed in at least this fraction of cells in the test group."/> + <param name="max_out_group_fraction" type="float" min="0.0" max="1.0" value="0.5" label="Maximum out-group fraction" + help="Post-test filtering to only keep genes expressed in at most this fraction of cells in the reference group."/> + <param name="min_fold_change" type="float" value="2" label="Minimum fold change" + help="Post-test filtering to only keep genes with at least this fold change of expression relative to the reference group."/> + </when> + </conditional> <param name="pts" argument="--pts" type="boolean" checked="false" label="Compute the fraction of cells expressing the genes?" truevalue="--pts" falsevalue="" /> <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=""/> </when> |