Mercurial > repos > bgruening > hicexplorer_chicdifferentialtest

annotate chicDifferentialTest.xml @ 7:eb8d8a1ac0e4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
author iuc
date Mon, 01 Jul 2024 19:01:27 +0000
parents 542a781235a0
children
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eb8d8a1ac0e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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1 <tool id="hicexplorer_chicdifferentialtest" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>computes differential interactions of viewpoints</description>
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3 <macros>
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4 <token name="@BINARY@">chicDifferentialTest</token>
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5 <import>macros.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 #import re
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10 @BINARY@
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11 --aggregatedFile $aggregatedFile
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12 --statisticTest $statisticTest_selector
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13 --alpha $alpha
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14 --outFileName differentialFile.hdf5
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15 --threads @THREADS@
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16
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17 ]]> </command>
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18 <inputs>
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19 <param name="aggregatedFile" type="data" format="h5" label="The aggregated data file created by chicAggregateStatistic" />
eb8d8a1ac0e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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20 <param name="alpha" type="float" value="2.0" label="Alpha" help="Accept all samples to significance level alpha." />
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21 <param name="statisticTest_selector" type="select" label="Statistical test">
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22 <option value="fisher" selected="True">Fisher exact</option>
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23 <option value="chi2">Chi2 contingency</option>
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24 </param>
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25 </inputs>
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26 <outputs>
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27 <data name="differentialFile" from_work_dir="differentialFile.hdf5" format="h5" label="Differential test file" />
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="aggregatedFile" value="cHi-C/chicAggregateStatistic/aggregate.hdf5" />
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32 <param name="statisticTest_selector" value="chi2" />
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33 <param name="alpha" value="0.5" />
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34 <output name="differentialFile" ftype="h5">
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35 <assert_contents>
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36 <has_h5_attribute key="type" value="differential" />
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37 </assert_contents>
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38 </output>
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39 </test>
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40 </tests>
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41 <help><![CDATA[
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43 Differential testing of two viewpoints
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44 ======================================
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45
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46 chicDifferentialTest tests if two locations under consideration of the reference point have a different interaction count. Either Fisher's test or chi2 contingency test can be used.
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47 Input files for this test can be created with `chicAggregateStatistic`. H0 is assuming the interactions are not different. Therefore the differential interaction counts are all where H0 was rejected.
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50 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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52 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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53 ]]> </help>
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54 <expand macro="citations" />
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55 </tool>