Mercurial > repos > iuc > schicexplorer_schiccreatebulkmatrix

annotate scHicCreateBulkMatrix.xml @ 1:69d511922826 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d
author iuc
date Fri, 14 Apr 2023 14:18:04 +0000
parents 0c8df7ecec37
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69d511922826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d
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1 <tool id="schicexplorer_schiccreatebulkmatrix" name="@BINARY@" version="@TOOL_VERSION@.1" profile="@PROFILE@">
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2 <description>creates the bulk matrix out of single-cell Hi-C interaction matrices</description>
0c8df7ecec37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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3 <macros>
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4 <token name="@BINARY@">scHicCreateBulkMatrix</token>
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5 <import>macros.xml</import>
0c8df7ecec37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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6 </macros>
0c8df7ecec37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 @BINARY@
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11 --matrix '$matrix_scooler'
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13 --outFileName bulk_matrix.cool
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0c8df7ecec37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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15 --threads @THREADS@
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17 ]]></command>
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18 <inputs>
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20 <expand macro="matrix_scooler_macro"/>
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21 </inputs>
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22 <outputs>
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69d511922826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d
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23 <data name="outFileName" from_work_dir="bulk_matrix.cool" format="scool" label="${tool.name} on ${on_string}: Bulk matrix"/>
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name='matrix_scooler' value='test_matrix.scool' />
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69d511922826 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d
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28 <output name="outFileName" file="scHicCreateBulkMatrix/bulk_matrix.cool" ftype="scool" compare="sim_size" delta="4000"/>
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29 </test>
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30 </tests>
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31 <help><![CDATA[
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33 Create bulk matrix
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34 ==================
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36 scHicCreateBulkMatrix adds all available single-cell matrices of a scool file together and writes it as a single matrix to a cool file.
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38 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
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40 .. _readthedocs.io: http://schicexplorer.readthedocs.io/
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41 ]]></help>
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42 <expand macro="citations" />
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44 </tool>