Mercurial > repos > ebi-gxa > scanpy_scale_data
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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
author | ebi-gxa |
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date | Tue, 27 Feb 2024 16:43:09 +0000 |
parents | bf30bd6355da |
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<?xml version="1.0" encoding="utf-8"?> <tool id="scanpy_scale_data" name="Scanpy ScaleData" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <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} @SAVE_MATRIX_OPTS@ @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"/> <expand macro="save_matrix_params"/> </inputs> <outputs> <expand macro="output_data_obj" description="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" ftype="h5"> <assert_contents> <has_h5_keys keys="var/mean"/> </assert_contents> </output> </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>