annotate peca.xml @ 9:f2b34bdd95fb draft

planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca
author caleb-easterly
date Mon, 05 Mar 2018 18:06:42 -0500
parents 56b8fbbe6e03
children f0de83932f9e
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f2b34bdd95fb planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca
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1 <tool id="peca" name="PECA" version="0.1.1">
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2 <description>probe-level expression change averaging</description>
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3 <requirements>
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4 <requirement type="package" version="1.14.0">bioconductor-peca</requirement>
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5 <requirement type="package" version="3.4.1">r-base</requirement>
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6 <!--<requirement type="package">r-dbi</requirement>-->
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7 </requirements>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ## write groups to file
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10 echo '$group1' > group1.txt &&
f50bb34c1a37 planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca
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11 echo '$group2' > group2.txt &&
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12 Rscript --vanilla '$__tool_directory__/peca.R' '$input' group1.txt group2.txt '$test_type' '$output'
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13 ]]></command>
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14 <inputs>
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15 <param name="input" type="data" format="tabular"/>
f50bb34c1a37 planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca
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16 <param name="group1" type="data_column" data_ref="input" multiple="true"/>
f50bb34c1a37 planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca
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17 <param name="group2" type="data_column" data_ref="input" multiple="true"/>
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18 <param name="test_type" type="select">
5a39fa8a235a planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca
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19 <option value="t" selected="true">Standard t-test</option>
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20 <option value="modt">Modified t-test</option>
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21 <option value="rots">Reproducibility-optimized test statistic</option>
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22 </param>
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23 </inputs>
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24 <outputs>
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25 <data format="tabular" name="output"/>
f50bb34c1a37 planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="input" value="test.tab" ftype="tabular"/>
f50bb34c1a37 planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca
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30 <param name="group1" value="2,3,4"/>
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31 <param name="group2" value="5,6,7"/>
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32 <param name="test_type" value="t"/>
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33 <output name="output" file="out.tab" ftype="tabular"/>
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34 </test>
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35 </tests>
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36 <help><![CDATA[
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37 ]]></help>
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38 </tool>