Mercurial > repos > ebi-gxa > scanpy_filter_genes
diff scanpy-filter-genes.xml @ 1:7aebd6265a97 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
author | ebi-gxa |
---|---|
date | Mon, 16 Sep 2019 08:15:32 -0400 |
parents | d1b97a5d5a8d |
children | a797a810d7e9 |
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--- a/scanpy-filter-genes.xml Wed Apr 03 11:10:01 2019 -0400 +++ b/scanpy-filter-genes.xml Mon Sep 16 08:15:32 2019 -0400 @@ -2,42 +2,50 @@ <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> + <import>scanpy_macros2.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ln -s '${input_obj_file}' input.h5 && -PYTHONIOENCODING=utf-8 scanpy-filter-genes.py - -i input.h5 - -f '${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@ +PYTHONIOENCODING=utf-8 scanpy-filter-genes +#if $parameters + #set pars = ' '.join(['--param {name} {min} {max}'.format(**$p) for $p in $parameters]) + ${pars} +#end if +#if $categories + #set cats = ' '.join(['--category {name} {values}'.format(**$c) for $c in $categories]) + ${cats} +#end if +#if $subsets + #set subs = ' '.join(['--subsets {name} {subset}'.format(**$s) for $c in $subsets]) + ${subs} +#end if + @INPUT_OPTS@ + @OUTPUT_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"> + + <repeat name="parameters" title="Parameters used to filter cells" min="1"> + <param name="name" type="text" value="n_cells" label="Name of parameter to filter on" help="for example n_genes or n_counts"> <option value="n_cells">n_cells</option> - <option value="n_counts">n_counts</option> + <option value="gene: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"/> + <param name="min" type="float" min="0" value="0" label="Min value"/> + <param name="max" type="float" min="0" 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"/> + + <repeat name="categories" title="Categories used to filter genes" min="0"> + <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/> + <param name="values" type="text" value="" label="Comma-separated values"/> + </repeat> + + <repeat name="subsets" title="Subsets used to filter genes" min="0"> + <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/> + <param name="subset" type="data" format="tabular" label="List of values"/> + </repeat> <expand macro="export_mtx_params"/> </inputs> @@ -57,7 +65,7 @@ <param name="max" value="1e9"/> </repeat> <repeat name="parameters"> - <param name="name" value="n_counts"/> + <param name="name" value="gene:n_counts"/> <param name="min" value="0"/> <param name="max" value="1e9"/> </repeat>