Mercurial > repos > ebi-gxa > scanpy_parameter_iterator
view scanpy-parameter-iterator.xml @ 15:fb354a78d4ae draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 2db9e8cecb8d373874318e53ec2d4d7a64dd1b24-dirty"
author | ebi-gxa |
---|---|
date | Fri, 11 Sep 2020 11:04:24 +0000 |
parents | 7c4d44c14ceb |
children | ae4debc68f4a |
line wrap: on
line source
<tool id="scanpy_parameter_iterator" name="Scanpy ParameterIterator" version="0.0.1+galaxy2"> <description>produce an iteration over a defined parameter</description> <macros> <import>scanpy_macros.xml</import> </macros> <requirements> <requirement type="package" version="1.42.1">bioconductor-rtracklayer</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ mkdir outputs; #if str( $input_type.parameter_values ) == "list_comma_separated_values": for param in \$(echo '$input_type.input_values' | sed 's/,/ /g'); do echo \$param > outputs/'$parameter_name'_\$param\.txt; done #else if str( $input_type.parameter_values ) == "step_increase_values": for param in \$(seq '$input_type.start_value' '$input_type.step' '$input_type.end_value'); do echo \$param > outputs/'$parameter_name'_\$param\.txt; done #end if ]]></command> <inputs> <param type="select" name="parameter_name" label="Parameter name" help="Select a type of parameter"> <option value="perplexity" selected="True">Perplexity</option> <option value="resolution">Resolution</option> <option value="n_neighbors">Number of neighbors</option> </param> <conditional name="input_type"> <param type="select" name="parameter_values" label="Choose the format of the input values" help="step increase values or list of all the parameter values"> <option value="list_comma_separated_values" selected="True">List of all parameter values to be iterated</option> <option value="step_increase_values">Step increase values to be iterated</option> </param> <when value="list_comma_separated_values"> <param type="text" value="0.1, 0.3, 0.5, 0.7, 1.0, 2.0, 3.0, 4.0, 5.0" name="input_values" label="User input values" help="List of all comma separated values for the parameter"/> </when> <when value="step_increase_values"> <param type="float" value="1" name="start_value" label="Starting value" help="Initial value for the parameter"/> <param type="float" value="2" name="step" label="Step" help="Increment to use from first to last value"/> <param type="float" value="10" name="end_value" label="Ending value" help="Final value for the parameter. The final value is not included if increments of step don't match the last value."/> </when> </conditional> </inputs> <outputs> <collection name="parameter_iteration" type="list" label="Parameter iterated"> <discover_datasets pattern="__name_and_ext__" directory="outputs"/> </collection> </outputs> <tests> <test> <param name="parameter_name" value="perplexity"/> <conditional name="input_type"> <param name="parameter_values" value="list_comma_separated_values"/> <param name="input_values" value="1, 5, 10"/> </conditional> <output_collection name="parameter_iteration" count="3"> <element name="perplexity_1" file="perplexity_1.txt" ftype="txt" compare="sim_size"/> <element name="perplexity_5" file="perplexity_5.txt" ftype="txt" compare="sim_size"/> <element name="perplexity_10" file="perplexity_10.txt" ftype="txt" compare="sim_size"/> </output_collection> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** Given start, step and end, it will iterate parameters for either perplexity (for t-SNE), resolution (clustering) or number of neighbours (neighbour graph construction). **Inputs** * Parameter name: either Resolution or Perplexity. * Starting value: float for Resolution, integer for Perplexity. * Step: float for Resolution, integer for Perplexity. * End value: float for Resolution, integer for Perplexity. **Outputs** * Collection of parameters to be passed to either Scanpy run tSNE (perplexity) or Scanpy find clusters (resolution). @VERSION_HISTORY@ ]]></help> <expand macro="citations"/> </tool>