Mercurial > repos > ebi-gxa > scanpy_filter_cells
view scanpy-filter-cells.xml @ 0:9f0ca1641ab2 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
author | ebi-gxa |
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date | Wed, 03 Apr 2019 11:12:31 -0400 |
parents | |
children | dcfb23758646 |
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<?xml version="1.0" encoding="utf-8"?> <tool id="scanpy_filter_cells" name="Scanpy FilterCells" version="@TOOL_VERSION@+galaxy0"> <description>based on counts and numbers of genes expressed</description> <macros> <import>scanpy_macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ln -s '${input_obj_file}' input.h5 && PYTHONIOENCODING=utf-8 scanpy-filter-cells.py -i input.h5 -f '${input_format}' -o output.h5 -F '${output_format}' #if $parameters #set pars = ','.join([str($p['name']) for $p in $parameters]) -p '${pars}' #set mins = ','.join([str($p['min']) for $p in $parameters]) -l '${mins}' #set maxs = ','.join([str($p['max']) for $p in $parameters]) -j '${maxs}' #end if #if $subset -s '${subset}' #end if ]]></command> <inputs> <expand macro="input_object_params"/> <expand macro="output_object_params"/> <repeat name="parameters" title="Parameters used to filter cells" min="1"> <param name="name" type="text" value="n_genes" label="Name of parameter to filter on" help="for example n_genes or n_counts"> <option value="n_genes">n_genes</option> <option value="n_counts">n_counts</option> </param> <param name="min" type="float" value="0" min="0" label="Min value"/> <param name="max" type="float" value="1e9" label="Max value"/> </repeat> <param name="subset" argument="--subset-list" type="data" format="tsv" optional="true" label="List of barcodes"/> </inputs> <outputs> <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Filtered cells"/> </outputs> <tests> <test> <param name="input_obj_file" value="read_10x.h5"/> <param name="input_format" value="anndata"/> <param name="output_format" value="anndata"/> <repeat name="parameters"> <param name="name" value="n_genes"/> <param name="min" value="200"/> <param name="max" value="2500"/> </repeat> <repeat name="parameters"> <param name="name" value="n_counts"/> <param name="min" value="0"/> <param name="max" value="1e9"/> </repeat> <output name="output_h5" file="filter_cells.h5" ftype="h5" compare="sim_size"/> </test> </tests> <help><![CDATA[ ======================================================================================== Filter cells outliers based on counts and numbers of genes expressed (`pp.filter_cells`) ======================================================================================== For instance, only keep cells with at least `min_counts` counts or `min_genes` genes expressed. This is to filter measurement outliers, i.e., "unreliable" observations. @HELP@ @VERSION_HISTORY@ ]]></help> <expand macro="citations"/> </tool>