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view scanpy-filter-genes.xml @ 0:d1b97a5d5a8d 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 11:10:01 -0400 |
parents | |
children | 7aebd6265a97 |
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<?xml version="1.0" encoding="utf-8"?> <tool id="scanpy_filter_genes" name="Scanpy FilterGenes" version="@TOOL_VERSION@+galaxy1"> <description>based on counts and numbers of cells expressed</description> <macros> <import>scanpy_macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ln -s '${input_obj_file}' input.h5 && PYTHONIOENCODING=utf-8 scanpy-filter-genes.py -i input.h5 -f '${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 @EXPORT_MTX_OPTS@ ]]></command> <inputs> <expand macro="input_object_params"/> <expand macro="output_object_params"/> <repeat name="parameters" title="Parameters used to filter genes" min="1"> <param name="name" type="text" value="n_cells" label="Name of parameter to filter on" help="for example n_cells or n_counts"> <option value="n_cells">n_cells</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 gene IDs or symbols"/> <expand macro="export_mtx_params"/> </inputs> <outputs> <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Filtered genes"/> <expand macro="export_mtx_outputs"/> </outputs> <tests> <test> <param name="input_obj_file" value="filter_cells.h5"/> <param name="input_format" value="anndata"/> <param name="output_format" value="anndata"/> <repeat name="parameters"> <param name="name" value="n_cells"/> <param name="min" value="3"/> <param name="max" value="1e9"/> </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_genes.h5" ftype="h5" compare="sim_size"/> </test> </tests> <help><![CDATA[ =================================================================== Filter genes based on number of cells or counts (`pp.filter_genes`) =================================================================== Keep genes that have at least `min_counts` counts or are expressed in at least `min_cells` cells or have at most `max_counts` counts or are expressed in at most `max_cells` cells. Only provide one of the optional parameters `min_counts`, `min_cells`, `max_counts`, `max_cells` per call. @HELP@ @VERSION_HISTORY@ ]]></help> <expand macro="citations"/> </tool>