Mercurial > repos > iuc > schicexplorer_schicinfo

annotate scHicInfo.xml @ 1:09f8be8a6e76 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
author iuc
date Tue, 10 Mar 2020 15:10:08 -0400
parents 35c211c5146d
children 41b415c410e3
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35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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1 <tool id="schicexplorer_schicinfo" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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09f8be8a6e76 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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2 <description>information about a single-cell scool matrix</description>
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3 <macros>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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4 <token name="@BINARY@">scHicInfo</token>
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5 <import>macros.xml</import>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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6 </macros>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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7 <expand macro="requirements" />
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09f8be8a6e76 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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8 <command detect_errors="exit_code"><![CDATA[
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9 @BINARY@
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10 --matrix '$matrix_scooler'
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11 >> matrices_info.txt
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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12 ]]></command>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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13 <inputs>
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09f8be8a6e76 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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14 <expand macro="matrix_scooler_macro"/>
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15 </inputs>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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16 <outputs>
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17 <data name="outFileName" from_work_dir="matrices_info.txt" format="txt" label="${tool.name} on ${on_string}: Matrix Info"/>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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18 </outputs>
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19 <tests>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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20 <test>
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21 <param name='matrix_scooler' value='test_matrix.scool' />
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22 <output name="outFileName" file="scHicInfo/matrices_info.txt" ftype="txt" compare="sim_size" delta="4000"/>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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23 </test>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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24 </tests>
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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25 <help><![CDATA[
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35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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27 Consensus matrices
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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28 ==================
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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29
1
09f8be8a6e76 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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30 scHicInfo gives information about the provided single-cell Hi-C scool file. For example:
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35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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32 .. code-block::
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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33
1
09f8be8a6e76 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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34 Filename: nagano2017_raw.scool
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35 Contains 3882 single-cell matrices
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36 The information stored via cooler.info of the first cell is:
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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37
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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38 bin-size 1000000
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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39 bin-type fixed
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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40 creation-date 2019-05-16T11:46:31.826214
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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41 format HDF5::Cooler
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42 format-url https://github.com/mirnylab/cooler
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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43 format-version 3
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44 generated-by cooler-0.8.3
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45 genome-assembly unknown
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46 metadata {}
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47 nbins 2744
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48 nchroms 35
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49 nnz 55498
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50 storage-mode symmetric-upper
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51 sum 486056
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52
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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53 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
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54
35c211c5146d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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55 .. _readthedocs.io: http://schicexplorer.readthedocs.io/
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56 ]]></help>
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57 <expand macro="citations" />
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58
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59 </tool>