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view scanpy-find-markers.xml @ 24:0a8e527d1517 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit cecd3663ae841b026216f01003d58ea7c3bfde3e-dirty"
author | ebi-gxa |
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date | Tue, 03 Aug 2021 08:58:41 +0000 |
parents | a6a896082cd7 |
children | a57c0538e56b |
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<?xml version="1.0" encoding="utf-8"?> <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> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ln -s '${input_obj_file}' input.h5 && PYTHONIOENCODING=utf-8 scanpy-find-markers #if $output_markers --save diffexp.tsv #end if --n-genes '${n_genes}' #if $groupby_file #set f = open($groupby_file.__str__) #set groupby = f.read().strip() #silent f.close #else #set groupby = $groupby.replace('INPUT_OBJ', $input_obj_file.__getattr__('name')) #end if --groupby '${groupby}' #if $settings.default == "false" #if $settings.key_added #set key_added = $settings.key_added.replace('GROUPBY', $groupby.__str__) --key-added '${key_added}' #end if --method '${settings.method}' ${settings.use_raw} ${settings.rankby_abs} #if $settings.groups --groups '${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}' $settings.pts $settings.tie_correct #end if @INPUT_OPTS@ @OUTPUT_OPTS@ ]]></command> <inputs> <expand macro="input_object_params"/> <expand macro="output_object_params"/> <param name="output_markers" type="boolean" checked="true" label="Output markers table in tsv format"/> <param name="n_genes" argument="--n-genes" type="integer" value="50" label="Number of top genes to show per group/cluster"/> <param name="groupby" argument="--groupby" type="text" value="louvain" label="The sample grouping/clustering to use."/> <param name="groupby_file" argument="--groupby" type="data" format="txt,tsv" optional="true" label="File with groupby. Overrides the groupby setting"/> <conditional name="settings"> <param name="default" type="boolean" checked="true" label="Use programme defaults"/> <when value="true"/> <when value="false"> <param name="key_added" argument="--key-added" type="text" optional="true" label="The key in adata.uns information is saved to. If included, the keyword 'GROUPBY' will be substituted with the value of the groupby setting."/> <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="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"/> <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="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."/> <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> <outputs> <expand macro="output_data_obj" description="Marker genes"/> <data name="output_tsv" format="tabular" from_work_dir="diffexp.tsv" label="${tool.name} on ${on_string}: Marker table"> <filter>output_markers</filter> </data> </outputs> <tests> <test> <param name="input_obj_file" value="louvain_1.0"/> <param name="input_format" value="anndata"/> <param name="output_format" value="anndata"/> <param name="output_tsv" value="true"/> <param name="n_genes" value="50"/> <param name="output_markers" value="true"/> <param name="default" value="false"/> <param name="groupby" value="INPUT_OBJ"/> <param name="key_added" value="GROUPBY_marker"/> <param name="method" value="t-test_overestim_var"/> <param name="rankby_abs" value="false"/> <output name="output_h5" file="find_markers.h5" ftype="h5" compare="sim_size"/> <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/> </test> <test> <param name="input_obj_file" value="louvain_1.0"/> <param name="input_format" value="anndata"/> <param name="output_format" value="anndata"/> <param name="output_tsv" value="true"/> <param name="n_genes" value="50"/> <param name="output_markers" value="true"/> <param name="default" value="false"/> <param name="groupby_file" value="groupby.txt"/> <param name="key_added" value="GROUPBY_marker"/> <param name="method" value="t-test_overestim_var"/> <param name="rankby_abs" value="false"/> <output name="output_h5" file="find_markers.h5" ftype="h5" compare="sim_size"/> <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/> </test> </tests> <help><![CDATA[ ============================================================= Rank genes for characterizing groups (`tl.rank_genes_groups`) ============================================================= Rank genes for characterizing groups. @HELP@ @VERSION_HISTORY@ ]]></help> <expand macro="citations"/> </tool>