Mercurial > repos > ebi-gxa > scater_filter
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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
author | ebi-gxa |
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date | Wed, 03 Apr 2019 11:47:32 -0400 |
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<tool id="scater_filter" name="Scater Filter" version="@TOOL_VERSION@+galaxy0"> <description>cells and genes based on pre-calculated stats and QC metrics</description> <macros> <import>scater_macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ scater-filter.R -i '${R_scater_qc}' -o '$R_scater_filtered' #if $cell_parameters #set cell_pars = ','.join([str($p['name']) for $p in $cell_parameters]) -s '${cell_pars}' #set cell_mins = ','.join([str($p['min']) for $p in $cell_parameters]) -l '${cell_mins}' #set cell_maxs = ','.join([str($p['max']) for $p in $cell_parameters]) -j '${cell_maxs}' #end if #if $feature_parameters #set ft_pars = ','.join([str($p['name']) for $p in $feature_parameters]) -t '${ft_pars}' #set ft_mins = ','.join([str($p['min']) for $p in $feature_parameters]) -m '${ft_mins}' #set ft_maxs = ','.join([str($p['max']) for $p in $feature_parameters]) -n '${ft_maxs}' #end if #if $cells_use: -c '$cells_use' #end if #if $cells_discard: -C '$cells_discard' #end if #if $features_use: -f '$features_use' #end if #if $output_selected_cells: -u '$selected_cells' #end if #if $output_selected_features: -v '$selected_featuers' #end if ]]></command> <inputs> <param name="R_scater_qc" type="data" format="rdata" help="A serialized SingleCellExperiment object file in RDS format."/> <repeat name="cell_parameters" title="Parameters used to filter cells" min="0"> <param name="name" type="text" value="total_features_by_counts" label="Name of the parameter to filter on" help="for example: total_features_by_counts, total_counts"> <option value="total_features_by_counts">total_features_by_counts</option> <option value="total_counts">total_counts</option> </param> <param name="min" type="float" value="-1e9" label="Min value"/> <param name="max" type="float" value="1e9" label="Max value"/> </repeat> <repeat name="feature_parameters" title="Parameters used to filter features" min="0"> <param name="name" type="text" value="n_cells_by_counts" label="Name of the parameter to filter on" help="for example: n_cells_by_counts, total_counts"> <option value="n_cells_by_counts">n_cells_by_counts</option> <option value="total_counts">total_counts</option> </param> <param name="min" type="float" value="-1e9" label="Min value"/> <param name="max" type="float" value="1e9" label="Max value"/> </repeat> <param name="cells_use" argument="--cells-use" type="data" format="txt" optional="true" label="List of cells to include (optional)" help="Text file with one cell per line providing cell names to use as a subset."/> <param name="cells_discard" argument="--cells-discard" type="data" format="txt" optional="true" label="List of cells to exclude (optional)" help="Text file with one cell per line providing cell names to discard as a subset."/> <param name="features_use" argument="--features-use" type="data" format="txt" optional="true" label="List of features to include (optional)" help="Text file with one features per line providing feature names to use as a subset."/> <param name="output_selected_cells" label="Output lists of pass-filter cells" type="boolean" checked="false"/> <param name="output_selected_features" label="Output lists of pass-filter features" type="boolean" checked="false"/> </inputs> <outputs> <data name="R_scater_filtered" format="rdata" label="${tool.name} on ${on_string}: serialized SingleCellExperiment object"/> <data name="selected_cells" format="tsv" label="${tool.name} on ${on_string}: pass-filter cells"> <filter>output_selected_cells</filter> </data> <data name="selected_featuers" format="tsv" label="${tool.name} on ${on_string}: pass-filter features"> <filter>output_selected_features</filter> </data> </outputs> <tests> <test> <param name="R_scater_qc" value="R_scater_qc.rds"/> <output name="R_scater_filtered" file="R_scater_filtered.rds"/> </test> </tests> <help><![CDATA[ @HELP@ @VERSION_HISTORY@ ]]></help> <expand macro="citations" /> </tool>