Mercurial > repos > ebi-gxa > scanpy_regress_variable
diff scanpy-regress-variable.xml @ 0:6c990f8ccad3 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
| author | ebi-gxa |
|---|---|
| date | Mon, 16 Sep 2019 08:22:16 -0400 |
| parents | |
| children | 203fac3b1ba3 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy-regress-variable.xml Mon Sep 16 08:22:16 2019 -0400 @@ -0,0 +1,48 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="scanpy_regress_variable" name="Scanpy RegressOut" version="@TOOL_VERSION@+galaxy0"> + <description>variables that might introduce batch effect</description> + <macros> + <import>scanpy_macros2.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +ln -s '${input_obj_file}' input.h5 && +PYTHONIOENCODING=utf-8 scanpy-regress + --keys '${variable_keys}' + @INPUT_OPTS@ + @OUTPUT_OPTS@ +]]></command> + + <inputs> + <expand macro="input_object_params"/> + <expand macro="output_object_params"/> + <param name="variable_keys" type="text" label="Variables to regress out" help="Use comma to separate multiple variables"/> + </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="variable_keys" value="n_counts"/> + <output name="output_h5" file="scale_data.h5" ftype="h5" compare="sim_size"/> + </test> + </tests> + + <help><![CDATA[ + .. class:: infomark + + **What it does** + + Regress out unwanted source of variance (`scanpy.pp.regress_out`) + + @HELP@ + + @VERSION_HISTORY@ +]]></help> + <expand macro="citations"/> +</tool>