Mercurial > repos > ebi-gxa > scanpy_scale_data
view scanpy-scale-data.xml @ 0:96b851e96dd0 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
author | ebi-gxa |
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date | Wed, 03 Apr 2019 11:09:38 -0400 |
parents | |
children | 9acb5f068e6b |
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<?xml version="1.0" encoding="utf-8"?> <tool id="scanpy_scale_data" name="Scanpy ScaleData" version="@TOOL_VERSION@+galaxy1"> <description>to make expression variance the same for all genes</description> <macros> <import>scanpy_macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ln -s '${input_obj_file}' input.h5 && PYTHONIOENCODING=utf-8 scanpy-scale-data.py -i input.h5 -f '${input_format}' -o output.h5 -F '${output_format}' #if $scale_max -x '${scale_max}' #end if #if $var_to_regress -V '${var_to_regress}' #end if #if $do_log --do-log #end if #if $zero_center --zero-center #end if ]]></command> <inputs> <expand macro="input_object_params"/> <expand macro="output_object_params"/> <param name="do_log" argument="--do-log" type="boolean" checked="true" label="Do log(x+1) transformation"/> <param name="zero_center" argument="--zero-center" type="boolean" checked="true" label="Zero center data before scaling"/> <param name="var_to_regress" argument="--var-to-regress" type="text" optional="true" label="Variable(s) to regress out"> <option value="n_counts">n_counts</option> </param> <param name="scale_max" argument="--scale-max" type="float" optional="true" label="Truncate to this value after scaling"/> </inputs> <outputs> <data name="output_h5" format="h5" from_work_dir="output.h5" label="${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="do_log" value="true"/> <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 zero mean (`pp.scale`) Regress out unwanted sources of variation (`pp.regress_out`) Regress out unwanted sources of variation, using simple linear regression. This is inspired by Seurat's `regressOut` function in R. @HELP@ @VERSION_HISTORY@ ]]></help> <expand macro="citations"/> </tool>