Mercurial > repos > ebi-gxa > scanpy_scale_data
view scanpy-scale-data.xml @ 3:4c73b070cbff draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit d13a0a5fceabe51e1a6fe763767b963623aa295a
author | ebi-gxa |
---|---|
date | Mon, 28 Oct 2019 05:24:01 -0400 |
parents | 9acb5f068e6b |
children | c23efca79651 |
line wrap: on
line source
<?xml version="1.0" encoding="utf-8"?> <tool id="scanpy_scale_data" name="Scanpy ScaleData" version="@TOOL_VERSION@+galaxy0"> <description>to make expression variance the same for all genes</description> <macros> <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-scale-data #if $scale_max --max-value '${scale_max}' #end if ${zero_center} @INPUT_OPTS@ @OUTPUT_OPTS@ ]]></command> <inputs> <expand macro="input_object_params"/> <expand macro="output_object_params"/> <param name="zero_center" type="boolean" checked="true" truevalue="" falsevalue="--no-zero-center" label="Zero center data before scaling"/> <param name="scale_max" argument="--max-value" type="float" min="0" optional="true" label="Truncate to this value after scaling"/> </inputs> <outputs> <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Scaled data"/> </outputs> <tests> <test> <param name="input_obj_file" value="find_variable_genes.h5"/> <param name="input_format" value="anndata"/> <param name="output_format" value="anndata"/> <param name="zero_center" value="true"/> <param name="scale_max" value="10"/> <output name="output_h5" file="scale_data.h5" ftype="h5" compare="sim_size"/> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** Scale data to unit variance and (optionally) zero mean (`scanpy.pp.scale`) @HELP@ @VERSION_HISTORY@ ]]></help> <expand macro="citations"/> </tool>