Mercurial > repos > iuc > schicexplorer_schicplotclusterprofiles
annotate scHicPlotClusterProfiles.xml @ 3:0aca9bf1e402 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit c535679b4086f5bd1a75e9765b8708bf1bd2d81b
| author | iuc |
|---|---|
| date | Thu, 31 Jul 2025 16:50:19 +0000 |
| parents | 65f2f5d29947 |
| children |
| rev | line source |
|---|---|
|
2
65f2f5d29947
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d
iuc
parents:
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1 <tool id="schicexplorer_schicplotclusterprofiles" name="@BINARY@" version="@TOOL_VERSION@.1" profile="@PROFILE@"> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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2 <description>plot single-cell Hi-C interaction matrices cluster profiles</description> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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3 <macros> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff
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4 <token name="@BINARY@">scHicPlotClusterProfiles</token> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff
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5 <import>macros.xml</import> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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6 </macros> |
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3
0aca9bf1e402
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit c535679b4086f5bd1a75e9765b8708bf1bd2d81b
iuc
parents:
2
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7 <expand macro="xrefs"/> |
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0
2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff
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8 <expand macro="requirements" /> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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9 <command detect_errors="exit_code"><![CDATA[ |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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10 @BINARY@ |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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11 |
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9da580a74230
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
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12 --matrix $matrix_scooler |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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13 --clusters $clusters |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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14 #if $chromosomes: |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff
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15 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ]) |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff
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16 --chromosomes $chromosome |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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17 #end if |
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3
0aca9bf1e402
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit c535679b4086f5bd1a75e9765b8708bf1bd2d81b
iuc
parents:
2
diff
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18 |
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0
2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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19 #if $order_by_conditional.order_by_selection == 'orderByFile': |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff
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20 --orderBy $order_by_conditional.order_by_selection |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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21 #elif $order_by_conditional.order_by_selection == 'svl': |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff
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22 --orderBy $order_by_conditional.order_by_selection |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff
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23 --distanceShortRange $order_by_conditional.distanceShortRange |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff
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24 --distanceLongRange $order_by_conditional.distanceLongRange |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff
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25 #end if |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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26 #if $dpi: |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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27 --dpi $dpi |
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3
0aca9bf1e402
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit c535679b4086f5bd1a75e9765b8708bf1bd2d81b
iuc
parents:
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28 #end if |
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0
2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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29 --outFileName plot.$image_file_format |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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30 |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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31 --threads @THREADS@ |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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32 |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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33 && mv plot.$image_file_format plot |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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34 |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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35 ]]></command> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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36 <inputs> |
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1
9da580a74230
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents:
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37 <expand macro="matrix_scooler_macro"/> |
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0
2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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38 <param name='clusters' type='data' format='txt' label='Cluster file' help='Cluster file created by scHicCluster, scHicClusterCompartments, scHicClusterMinHash or scHicClusterSVL'/> |
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3
0aca9bf1e402
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit c535679b4086f5bd1a75e9765b8708bf1bd2d81b
iuc
parents:
2
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39 <param name="maximalDistance" type="integer" value="2000000" label="Maximal distance" help='Maximal distance to consider for plotting' /> |
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0
2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
diff
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40 <conditional name="order_by_conditional"> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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41 <param name='order_by_selection' label='Order samples by' type='select'> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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42 <option value='svl' selected='true'>Short vs long range ratio</option> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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43 <option value='orderByFile'>Order by file</option> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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44 </param> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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45 <when value='svl' > |
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3
0aca9bf1e402
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit c535679b4086f5bd1a75e9765b8708bf1bd2d81b
iuc
parents:
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46 <param name="distanceShortRange" type="integer" value="2000000" label="Distance short range" help='Distance for the short range to compute the ratio of sum (short range interactions) / sum (long range interactions)' /> |
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0aca9bf1e402
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit c535679b4086f5bd1a75e9765b8708bf1bd2d81b
iuc
parents:
2
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47 <param name="distanceLongRange" type="integer" value="12000000" label="Distance long range" help='Distance for the long range to compute the ratio of sum (short range interactions) / sum (long range interactions)' /> |
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0
2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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48 </when> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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49 <when value='orderByFile'> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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50 </when> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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51 </conditional> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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52 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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53 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/> |
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0aca9bf1e402
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit c535679b4086f5bd1a75e9765b8708bf1bd2d81b
iuc
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54 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
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55 <param name="image_file_format" type="select" label="Image output format"> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
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56 <option value="png" selected="True">png</option> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
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57 <option value="svg">svg</option> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
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58 <option value="pdf">pdf</option> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
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59 </param> |
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0aca9bf1e402
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit c535679b4086f5bd1a75e9765b8708bf1bd2d81b
iuc
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60 |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
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61 </inputs> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
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62 <outputs> |
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9da580a74230
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
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63 <data name='output_plot' from_work_dir='plot' format='png' label='Cluster profile plot on ${on_string} '> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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64 <change_format> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
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65 <when input="image_file_format" value="svg" format="svg" /> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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66 <when input="image_file_format" value="pdf" format="pdf" /> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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67 </change_format> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
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68 </data> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
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69 </outputs> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
parents:
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70 <tests> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
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71 <test> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
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72 <param name='matrix_scooler' value='test_matrix.scool' /> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
iuc
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73 <param name='clusters' value='scHicPlotClusterProfiles/cluster_kmeans.txt' /> |
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2427c6d8cdd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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74 <conditional name="order_by_conditional"> |
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75 <param name="order_by_selection" value="svl"/> |
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76 <param name="distanceShortRange" value="2000000" /> |
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77 <param name="distanceLongRange" value="12000000" /> |
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78 </conditional> |
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79 <param name="maximalDistance" value="50000000" /> |
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80 <param name="image_file_format" value="png" /> |
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81 <param name="dpi" value="300" /> |
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82 |
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83 <output name="output_plot" file="scHicPlotClusterProfiles/plot.png" ftype="png" compare="sim_size" delta="35000"/> |
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84 </test> |
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85 |
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86 </tests> |
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87 <help><![CDATA[ |
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88 |
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89 Plot cluster profiles |
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90 ===================== |
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91 |
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92 scHicPlotClusterProfiles plots the profile of each scHi-C interaction matrix associated to a cluster, within the cluster the matrices can be ordered either via their short vs long range ratio or by the order of the file. |
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93 This tool is useful as a quality control of a cluster to check if all matrices assigned to that cluster are displaying similar contacts distribution. |
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94 |
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95 .. image:: $PATH_TO_IMAGES/clusters_svl_spectral.png |
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96 :width: 50% |
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97 |
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98 For more information about scHiCExplorer please consider our documentation on readthedocs.io_ |
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99 |
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100 .. _readthedocs.io: http://schicexplorer.readthedocs.io/ |
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101 ]]></help> |
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102 <expand macro="citations" /> |
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103 |
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104 </tool> |