Mercurial > repos > iuc > scater_normalize

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 08:34:09 +0000
parents 0cb9a5f830fc
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0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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1 <tool id="scater_normalize" name="Scater: normalize SCE" version="@TOOL_VERSION@">
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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2 <description>Compute normalised expression values for SCE</description>
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7318ad060d7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <expand macro="bio_tools"/>
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0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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4 <macros>
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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5 <import>macros.xml</import>
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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6 </macros>
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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7 <expand macro="requirements" />
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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8 <command detect_errors="exit_code"><![CDATA[
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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9 Rscript '$__tool_directory__/scater-normalize.R'
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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10 -i '$input_loom'
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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11 -o '$output_loom'
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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12 ]]></command>
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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13 <inputs>
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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14 <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset to normalize" />
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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15 </inputs>
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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16 <outputs>
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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17 <data name="output_loom" format="loom" label="${tool.name} on ${on_string}" />
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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18 </outputs>
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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19 <tests>
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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20 <test>
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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21 <param name="input_loom" value="scater_manual_filtered.loom" ftype="loom" />
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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22 <output name="output_loom" file="scater_filtered_normalised.loom" compare="sim_size" />
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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23 </test>
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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24 </tests>
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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25 <help><![CDATA[
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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26 Normalize a SingleCellLoomExperiment object using Scater. Adds 'logcounts' to assays slot.
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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27 ]]></help>
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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28 <expand macro="citations" />
0cb9a5f830fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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29 </tool>