Mercurial > repos > ebi-gxa > scanpy_find_markers
changeset 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 | af9cf232d6c9 |
| children | c6fb86cc7de5 |
| files | scanpy-find-markers.xml scanpy_macros2.xml |
| diffstat | 2 files changed, 10 insertions(+), 4 deletions(-) [+] |
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--- a/scanpy-find-markers.xml Fri Jun 05 09:12:18 2020 -0400 +++ b/scanpy-find-markers.xml Mon Sep 07 13:05:52 2020 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@"> +<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>to find differentially expressed genes between groups</description> <macros> <import>scanpy_macros2.xml</import> @@ -22,7 +22,8 @@ #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}' -#end if + #end if + $settings.pts $settings.tie_correct @INPUT_OPTS@ @OUTPUT_OPTS@ ]]></command> @@ -55,6 +56,8 @@ 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."/> + <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> </conditional> </inputs>
--- a/scanpy_macros2.xml Fri Jun 05 09:12:18 2020 -0400 +++ b/scanpy_macros2.xml Mon Sep 07 13:05:52 2020 +0000 @@ -1,10 +1,13 @@ <macros> - <token name="@TOOL_VERSION@">1.4.3</token> + <token name="@TOOL_VERSION@">1.6.0</token> <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token> <token name="@PROFILE@">18.01</token> <token name="@VERSION_HISTORY@"><![CDATA[ **Version history** +1.6.0+galaxy0: Update to scanpy-scripts 0.2.13 (running scanpy ==1.6.0) to incorporate new options, code simplifications, and batch integration methods. Jonathan Manning, Expression Atlas team https://www.ebi.ac.uk/gxa/home at +EMBL-EBI https://www.ebi.ac.uk/ + 1.4.3+galaxy10: Update to scanpy-scripts 0.2.10 (running scanpy ==1.4.3) to address bugfixes in run-pca. 1.4.3+galaxy10: Update to scanpy-scripts 0.2.9 (running scanpy ==1.4.3) to address bugfixes in find-variable-genes. @@ -46,7 +49,7 @@ <xml name="requirements"> <requirements> - <requirement type="package" version="0.2.10">scanpy-scripts</requirement> + <requirement type="package" version="0.3.0">scanpy-scripts</requirement> <yield/> </requirements> </xml>