| Previous changeset 29:81c34e67f262 (2023-02-16) Next changeset 31:f0f78d29130f (2023-10-13) |
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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 d01fa18235ac692874cd3cfddef33696c2df8ac1-dirty |
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modified:
scanpy-find-markers.xml |
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| diff -r 81c34e67f262 -r 64259337506f scanpy-find-markers.xml --- a/scanpy-find-markers.xml Thu Feb 16 13:28:49 2023 +0000 +++ b/scanpy-find-markers.xml Sat Jul 15 08:44:51 2023 +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@+galaxy9" profile="@PROFILE@"> +<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy91" profile="@PROFILE@"> <description>to find differentially expressed genes between groups</description> <macros> <import>scanpy_macros2.xml</import> @@ -26,7 +26,6 @@ --key-added '${key_added}' #end if --method '${settings.method}' - ${settings.use_raw} ${settings.rankby_abs} #if $settings.groups --groups '${settings.groups}' @@ -35,6 +34,12 @@ #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 + #if $settings.layer + --layer '${settings.layer}' + --no-raw + #else + ${settings.use_raw} + #end if $settings.pts $settings.tie_correct #end if @INPUT_OPTS@ @@ -58,14 +63,16 @@ <param name="method" argument="--method" type="select" label="Method for testing differentially expressed genes"> <option value="t-test_overestim_var" selected="true">t-test with over-estimated variance</option> <option value="t-test">t-test</option> - <option value="wilcoxon">wilcoxon test, currently broken don't use</option> + <option value="wilcoxon">wilcoxon test</option> <option value="logreg">logistic regression</option> </param> <param name="use_raw" type="boolean" truevalue="--use-raw" falsevalue="--no-raw" checked="true" - label="Use raw attribute if present"/> + label="Use raw attribute if present" help="Uses adata.raw, usually what was available before processing. If the layer option is set, this will be ignored (raw will not be used)."/> <param name="rankby_abs" argument="--rankby_abs" type="boolean" truevalue="--rankby-abs" falsevalue="" checked="false" 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="groups" argument="--groups" optional="true" type="text" + label="Subset of groups/clusters to which comparisons should be restricted" + help="Comma separated list of groups existing within the groupby field in obs. Currently it fails if a single group is given, provide at least two."/> <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"/> <conditional name="filter"> <param name="default" type="boolean" checked="false" label="Use filtering defaults"/> @@ -79,6 +86,8 @@ 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="layer" argument="--layer" type="text" optional="true" label="Layer to use for marker genes computation" + help="The method prefers matrices/layers that are logged. Leave empty to use the default .X matrix. It will override the use of raw if set."/> <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> @@ -120,6 +129,22 @@ <param name="rankby_abs" value="false"/> <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/> </test> + <test> + <param name="input_obj_file" value="mnn.h5"/> + <param name="input_format" value="anndata"/> + <param name="n_genes" value="50"/> + <param name="output_markers" value="true"/> + <param name="default" value="false"/> + <param name="groupby" value="louvain"/> + <param name="key_added" value="l_markers"/> + <param name="method" value="wilcoxon"/> + <param name="layer" value="mnn"/> + <output name="output_h5ad" ftype="h5ad"> + <assert_contents> + <has_h5_keys keys="uns/l_markers_mnn"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ |