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 ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
author ebi-gxa
date Thu, 12 Mar 2020 09:09:35 +0000
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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="scanpy_scale_data" name="Scanpy ScaleData" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@">
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3 <description>to make expression variance the same for all genes</description>
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4 <macros>
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5 <import>scanpy_macros2.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '${input_obj_file}' input.h5 &&
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10 PYTHONIOENCODING=utf-8 scanpy-scale-data
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11 #if $scale_max
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edb0d2e8ab66 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
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12 --max-value '${scale_max}'
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13 #end if
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14 ${zero_center}
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15 @INPUT_OPTS@
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16 @OUTPUT_OPTS@
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17 ]]></command>
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19 <inputs>
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20 <expand macro="input_object_params"/>
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21 <expand macro="output_object_params"/>
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22 <param name="zero_center" type="boolean" checked="true" truevalue="" falsevalue="--no-zero-center"
edb0d2e8ab66 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
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23 label="Zero center data before scaling"/>
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24 <param name="scale_max" argument="--max-value" type="float" min="0" optional="true" label="Truncate to this value after scaling"/>
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25 </inputs>
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27 <outputs>
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28 <expand macro="output_data_obj" description="Scaled data"/>
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29 </outputs>
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31 <tests>
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32 <test>
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33 <param name="input_obj_file" value="find_variable_genes.h5"/>
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34 <param name="input_format" value="anndata"/>
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35 <param name="output_format" value="anndata"/>
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36 <param name="zero_center" value="true"/>
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37 <param name="scale_max" value="10"/>
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38 <output name="output_h5" file="scale_data.h5" ftype="h5" compare="sim_size"/>
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39 </test>
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40 </tests>
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42 <help><![CDATA[
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43 .. class:: infomark
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45 **What it does**
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46
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47 Scale data to unit variance and (optionally) zero mean (`scanpy.pp.scale`)
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49 @HELP@
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51 @VERSION_HISTORY@
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52 ]]></help>
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53 <expand macro="citations"/>
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54 </tool>