Mercurial > repos > ebi-gxa > scanpy_filter_cells
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy-filter-cells.xml Wed Apr 03 11:12:31 2019 -0400 @@ -0,0 +1,79 @@ +<?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>