Mercurial > repos > bgruening > hicexplorer_hicconvertformat

annotate hicConvertFormat.xml @ 9:afde92f1468f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 69bb60ab875c1c1769298678f0890d8b92f1899d
author iuc
date Thu, 05 Dec 2024 17:10:03 +0000
parents d3dc261a47ec
children
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d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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1 <tool id="hicexplorer_hicconvertformat" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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2 <description>Convert between different file formats</description>
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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3 <macros>
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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4 <token name="@BINARY@">hicConvertFormat</token>
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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5 <token name="@SINGLE_INPUT@">
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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6 #if $xml_path.inputFormat_selector == 'optionCool':
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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7 --matrices 'matrix.cool'
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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8 --inputFormat cool
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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9 #if $xml_path.correctionName:
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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10 --correction_name '$xml_path.correctionName'
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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11 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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12
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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13 #if $xml_path.correctionDivision:
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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14 --correction_division
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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15 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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16
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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17 #if $xml_path.chromosome:
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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18 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($xml_path.chromosome).split(' ') ])
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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19
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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20 --chromosome $chromosome
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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21 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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22
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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23 #if $xml_path.loadRawValues:
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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24 --load_raw_values
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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25 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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26 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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27 #if $xml_path.inputFormat_selector == 'optionH5':
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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28 --matrices "matrix.h5"
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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29 --inputFormat h5
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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30
1
e98b42e74a76 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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31 #end if
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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32 #if $xml_path.inputFormat_selector == 'optionHomer':
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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33 --matrices "matrix.homer"
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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34 --inputFormat homer
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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35
1
e98b42e74a76 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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36 #end if
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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37 #if $xml_path.inputFormat_selector == 'optionHicpro':
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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38 --matrices "matrix.hicpro"
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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39 --bedFileHicpro "matrix.bed"
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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40 --inputFormat hicpro
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e98b42e74a76 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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41 #end if
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d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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42 #if $xml_path.inputFormat_selector == 'option2Dtext':
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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43 --matrices "matrix.2Dtext"
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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44 #if $xml_path.resolutions:
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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45 #set $resolutions = ' '.join([ '"%s"' % $resolution for $resolution in str($xml_path.resolutions).split(" ") ])
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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46 --resolutions $resolutions
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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47 #end if
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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48 --chromosomeSizes "chromosomeSizes.txt"
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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49 --inputFormat 2D-text
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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50 #end if
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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51 #if $xml_path.inputFormat_selector == 'optionHic':
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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52 --matrices "matrix.hic"
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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53 #if $xml_path.resolutions:
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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54 #set $resolutions = ' '.join([ '"%s"' % $resolution for $resolution in str($xml_path.resolutions).split(" ") ])
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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55
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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56 --resolutions $resolutions
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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57 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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58 --inputFormat hic
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e98b42e74a76 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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59 #end if
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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60 </token>
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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61 <import>macros.xml</import>
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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62 </macros>
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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63
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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64 <expand macro="requirements" />
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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65 <command detect_errors="exit_code"><![CDATA[
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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66
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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67 ## single to single case
1
e98b42e74a76 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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68
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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69 #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'singleMatrix':
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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70 #set xml_path = $outputSingleMultiple_conditional.inputFormat_conditional
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71
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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72 #if $xml_path.inputFormat_selector == 'optionCool':
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ebf7f3397e79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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73 ln -s '$xml_path.matrix_h5_cooler' "matrix.cool" &&
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dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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74
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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75 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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76 #if $xml_path.inputFormat_selector == 'optionH5':
5
ebf7f3397e79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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77 ln -s '$xml_path.matrix_h5_cooler' "matrix.h5" &&
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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78
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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79 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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80 #if $xml_path.inputFormat_selector == 'optionHomer':
5
ebf7f3397e79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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81 ln -s '$xml_path.matrixHomer' "matrix.homer" &&
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dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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83 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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84
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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85 #if $xml_path.inputFormat_selector == 'optionHicpro':
5
ebf7f3397e79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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86 ln -s '$xml_path.matrixHicpro' "matrix.hicpro" &&
ebf7f3397e79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 1
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87 ln -s '$xml_path.bedHicpro' "matrix.bed" &&
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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88 #end if
7
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
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89 #if $xml_path.inputFormat_selector == 'option2Dtext':
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
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90 ln -s '$xml_path.matrix2Dtext' "matrix.2Dtext" &&
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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91
7
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
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92 ln -s '$xml_path.chromosomeSizes' "chromosomeSizes.txt" &&
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
93
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
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94 #end if
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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95 #if $xml_path.inputFormat_selector == 'optionHic':
5
ebf7f3397e79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 1
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96 ln -s '$xml_path.matrixHic' "matrix.hic" &&
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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97 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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98
1
e98b42e74a76 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents: 0
diff changeset
99 @BINARY@
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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100 @SINGLE_INPUT@
1
e98b42e74a76 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
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101
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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102 --outputFormat $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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103 --outFileName 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector'
7
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
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104 #if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'hicpro':
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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105 --bedFileHicpro intervalls.bed
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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106 #end if
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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107
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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108 ### Set up links to matrices to have correct ending
6
8e174d6160d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02
iuc
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109 #else if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix':
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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110 #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'resolution_option':
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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111 #set xml_path = $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.inputFormat_conditional
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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112 #if $xml_path.inputFormat_selector == 'optionCool':
5
ebf7f3397e79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 1
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113 ln -s '$xml_path.matrix_h5_cooler' "matrix.cool" &&
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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114 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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115
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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116 #if $xml_path.inputFormat_selector == 'optionH5':
5
ebf7f3397e79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 1
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117 ln -s '$xml_path.matrix_h5_cooler' "matrix.h5" &&
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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118 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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119
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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120 #if $xml_path.inputFormat_selector == 'optionHomer':
5
ebf7f3397e79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 1
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121 ln -s '$xml_path.matrix_h5_cooler' "matrix.homer" &&
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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122 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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123
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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124 #if $xml_path.inputFormat_selector == 'optionHicpro':
5
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iuc
parents: 1
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125 ln -s '$xml_path.matrix_h5_cooler' "matrix.hicpro" &&
ebf7f3397e79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 1
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126 ln -s '$xml_path.bedHicpro' "matrix.bed" &&
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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127 #end if
7
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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128 #if $xml_path.inputFormat_selector == 'option2Dtext':
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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129 ln -s '$xml_path.chromosomeSizes' "chromosomeSizes.txt" &&
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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130
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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131 #end if
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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132 #if $xml_path.inputFormat_selector == 'optionHic':
5
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133 ln -s '$xml_path.matrix_h5_cooler' "matrix.hic" &&
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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134 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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135 #else:
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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136 #set xml_manyToOne = $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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137 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionCool':
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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138 #for $counter, $m in enumerate($xml_manyToOne.matrix_h5_cooler_multiple):
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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139 ln -s '$m' "${counter}_matrix.cool" &&
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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140 #end for
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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141 #set $m = ' '.join([ '"%s_matrix"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrix_h5_cooler_multiple) ])
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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142
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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143 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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144 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionH5':
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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145 #for $counter, $m in enumerate($xml_manyToOne.matrix_h5_cooler_multiple):
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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146 ln -s '$m' "${counter}_matrix.h5" &&
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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147 #end for
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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148 #set $m = ' '.join([ '"%s_matrix"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrix_h5_cooler_multiple) ])
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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149 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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150 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHomer':
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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151 #for $counter, $m in enumerate($xml_manyToOne.matrixHomer):
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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152 ln -s '$m' "${counter}_matrix.homer" &&
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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153 #end for
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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154 #set $m = ' '.join([ '"%s_matrix.homer"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrixHomer) ])
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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155 #end if
7
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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156 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'option2Dtext':
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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157 #for $counter, $m in enumerate($xml_manyToOne.matrix2Dtext):
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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158 ln -s '$m' "${counter}_matrix.matrix2Dtext" &&
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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diff changeset
159 #end for
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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160 #set $m = ' '.join([ '"%s_matrix.matrix2Dtext"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrix2Dtext) ])
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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diff changeset
161 #if $xml_manyToOne.resolutions:
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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162 #set $resolutions = ' '.join([ '"%s"' % $resolution for $resolution in str($xml_manyToOne.resolutions).split(" ") ])
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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163 --resolutions $resolutions
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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164 #end if
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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165 --chromosomeSizes "chromosomeSizes.txt"
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
166
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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diff changeset
167 #end if
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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168 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHicpro':
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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169 #for $counter, $m in enumerate($xml_manyToOne.matrixHicpro):
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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170 ln -s '$m' "${counter}_matrix.hicpro" &&
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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171 #end for
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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172 #set $m = ' '.join([ '"%s_matrix.hicpro"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrixHicpro) ])
1
e98b42e74a76 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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173
0
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174 #for $counter, $bed in enumerate($xml_manyToOne.bedHicpro):
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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175 ln -s '$bed' "${counter}_matrix.bed" &&
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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176 #end for
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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177 #set $bed = ' '.join([ '"%s_matrix.bed"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.bedHicpro) ])
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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178 --bedFileHicpro '$bed'
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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179 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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180 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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181
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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182
1
e98b42e74a76 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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183 @BINARY@
0
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184 --outputFormat mcool
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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185
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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186 #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'resolution_option':
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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187 #set $resolutions = ' '.join([ '"%s"' % $resolution for $resolution in str($outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutions).split(" ") ])
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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188
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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189 --resolutions $resolutions
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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190 #if $xml_path.inputFormat_selector == 'optionCool':
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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191 --matrices "matrix.cool"
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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192 --inputFormat cool
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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193 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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194 #if $xml_path.inputFormat_selector == 'optionH5':
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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195 --matrices "matrix.h5"
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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196 --inputFormat h5
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197 #end if
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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198 #if $xml_path.inputFormat_selector == 'optionHomer':
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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199 --matrices "matrix.homer"
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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200 --inputFormat homer
1
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iuc
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201 #end if
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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202 #if $xml_path.inputFormat_selector == 'optionHicpro':
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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203 --matrices "matrix.hicpro"
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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204 --bedFileHicpro "matrix.bed"
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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205 --inputFormat hicpro
1
e98b42e74a76 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
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206 #end if
7
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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207 #if $xml_path.inputFormat_selector == 'option2Dtext':
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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208 --matrices "matrix.2Dtext"
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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209 --chromosomeSizes "chromosomeSizes.txt"
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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210 --inputFormat 2D-text
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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211 #end if
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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212 #if $xml_path.inputFormat_selector == 'optionHic':
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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213 --matrices "matrix.hic"
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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214 --inputFormat hic
1
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iuc
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215 #end if
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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216 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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217
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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218 #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'manyToOne_option':
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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219 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionCool':
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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220 --inputFormat cool
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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221 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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222
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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223 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionH5':
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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224 --inputFormat h5
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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225 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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226
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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227 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHomer':
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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228 --inputFormat homer
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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229 #end if
7
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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230 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'option2Dtext':
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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231
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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232 --inputFormat 2D-text
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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233 #end if
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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234 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHicpro':
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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235 --inputFormat hicpro
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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236 --bedFileHicpro '$bed'
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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237 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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238
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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239 --matrices $m
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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240 #end if
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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241 --outFileName matrix.mcool
6
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iuc
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242 #end if
8e174d6160d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02
iuc
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243 $storeAppliedCorrection
8e174d6160d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02
iuc
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244 $enforceInteger
8e174d6160d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02
iuc
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245
8e174d6160d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02
iuc
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246 #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'singleMatrix':
8e174d6160d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02
iuc
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247 #if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'ginteractions':
8e174d6160d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02
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248 && mv 'matrix.${outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector}.tsv' matrix_out
7
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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249 #else if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'hicpro':
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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250 && mv matrix.hicpro matrix_out
6
8e174d6160d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02
iuc
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251 #else:
8e174d6160d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02
iuc
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252 && mv 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector' matrix_out
8e174d6160d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02
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253 #end if
8e174d6160d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02
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254 #else if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix':
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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255 && mv matrix.mcool matrix_out
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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256 #end if
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257
0
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258 ]]>
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259 </command>
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260 <inputs>
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261 <conditional name="outputSingleMultiple_conditional">
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262 <param name="outputSingleMultiple_selector" type="select" label="Choose output matrix type">
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263 <option value="singleMatrix" selected="True">single matrix</option>
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264 <option value="multipleMatrix">multiple matrix</option>
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265 </param>
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266 <when value="singleMatrix">
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267 <expand macro="convertFormat_single_macro" />
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268 <expand macro="convertFormat_single_output_macro" />
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269 </when>
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270 <when value="multipleMatrix">
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271 <conditional name="resolutionOrManyToOne_conditional">
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272 <param name="resolutionOrManyToOne_selector" type="select" label="Choose input file type">
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273 <option value="resolution_option" >Create out of one matrix a multi matrix with diffrerent resolutions</option>
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274 <option value="manyToOne_option">Create out of n matrices one multi matrix</option>
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275 </param>
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276 <when value="resolution_option">
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277 <param name="resolutions" type="text" label="To be stored resolutions" help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
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278 <validator type="expression" message="Only numeric characters and a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
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279 </param>
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280 <expand macro="convertFormat_single_macro" />
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281 </when>
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282 <when value="manyToOne_option">
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283 <expand macro="convertFormat_multiple_macro" />
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284 </when>
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285 </conditional>
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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286 </when>
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287 </conditional>
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288 <param name="storeAppliedCorrection" type="boolean" truevalue="--store_applied_correction" falsevalue="" label="Store applied correction factors in column count" help="Option only for cool input files" />
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289 <param name="enforceInteger" type="boolean" truevalue="--enforce_integer" falsevalue="" label="Enforce integer for count column" help="Option only for cool input files" />
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290 </inputs>
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291 <outputs>
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292 <data name="output_converted_matrix" from_work_dir="matrix_out" format="cool" label="Converted matrix in cool format">
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293 <filter>outputSingleMultiple_conditional['outputSingleMultiple_selector'] == 'singleMatrix'</filter>
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294 <change_format>
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295 <when input="outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" value="h5" format="h5" />
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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296 <when input="outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" value="homer" format="zip" />
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297 <when input="outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" value="ginteractions" format="tabular" />
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298 <when input="outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" value="hicpro" format="tabular" />
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299 </change_format>
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300 </data>
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301 <data name="output_converted_matrix_bed" from_work_dir="intervalls.bed" format="tabular" label="Converted matrix in tabular format">
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302 <filter>outputSingleMultiple_conditional['outputFormat_conditional']['outputFormat_selector'] == 'hicpro'</filter>
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303 </data>
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304 <data name="output_converted_matrix_multi" from_work_dir="matrix_out" format="mcool" label="Converted matrix in mcool format">
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305 <filter>outputSingleMultiple_conditional['outputSingleMultiple_selector'] == 'multipleMatrix'</filter>
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306 </data>
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307 </outputs>
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308 <tests>
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309 <test expect_num_outputs="1">
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310 <conditional name="outputSingleMultiple_conditional">
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311 <param name="outputSingleMultiple_selector" value="singleMatrix" />
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312 <conditional name="inputFormat_conditional">
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313 <param name="inputFormat_selector" value="optionCool" />
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314 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
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315 </conditional>
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316
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317 <conditional name="outputFormat_conditional">
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318 <param name="outputFormat_selector" value="h5" />
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319 </conditional>
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320 </conditional>
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321 <output name="output_converted_matrix" ftype="h5">
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322 <assert_contents>
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323 <has_h5_keys keys="intervals,matrix,nan_bins" />
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324 </assert_contents>
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325 </output>
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326 </test>
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327 <test expect_num_outputs="1">
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328 <conditional name="outputSingleMultiple_conditional">
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329 <param name="outputSingleMultiple_selector" value="singleMatrix" />
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330 <conditional name="inputFormat_conditional">
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331 <param name="inputFormat_selector" value="option2Dtext" />
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332 <param name="matrix2Dtext" value="hicConvertFormat/GSM1436265_RAD21_ENCFF002EMQ.txt" />
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333 <param name="resolutions" value="10000" />
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334 <param name="chromosomeSizes" value="hicConvertFormat/hg19.chrom.sizes" />
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335 </conditional>
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336
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337 <conditional name="outputFormat_conditional">
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338 <param name="outputFormat_selector" value="h5" />
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339 </conditional>
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340 </conditional>
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341 <output name="output_converted_matrix" ftype="h5">
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
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diff changeset
342 <assert_contents>
7
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
343 <has_h5_keys keys="intervals,matrix" />
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
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diff changeset
344 </assert_contents>
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
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diff changeset
345 </output>
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
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diff changeset
346 </test>
7
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
347 <test expect_num_outputs="1">
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
348 <conditional name="outputSingleMultiple_conditional">
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
349 <param name="outputSingleMultiple_selector" value="singleMatrix" />
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
350 <conditional name="inputFormat_conditional">
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
351 <param name="inputFormat_selector" value="optionH5" />
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
352 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff changeset
353 </conditional>
1
e98b42e74a76 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents: 0
diff changeset
354
7
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
355 <conditional name="outputFormat_conditional">
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
356 <param name="outputFormat_selector" value="cool" />
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff changeset
357 </conditional>
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff changeset
358 </conditional>
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
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diff changeset
359 <output name="output_converted_matrix" ftype="cool">
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff changeset
360 <assert_contents>
7
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
361 <has_h5_keys keys="bins,chroms,indexes,pixels" />
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff changeset
362 </assert_contents>
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
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diff changeset
363 </output>
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff changeset
364 </test>
7
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
365 <test expect_num_outputs="1">
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
366 <conditional name="outputSingleMultiple_conditional">
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
367 <param name="outputSingleMultiple_selector" value="singleMatrix" />
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
368 <conditional name="inputFormat_conditional">
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
369 <param name="inputFormat_selector" value="optionCool" />
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
370 <param name="matrix_h5_cooler" value="hicConvertFormat/small_test_matrix_chr4.cool" />
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff changeset
371 </conditional>
1
e98b42e74a76 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents: 0
diff changeset
372
7
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
373 <conditional name="outputFormat_conditional">
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
374 <param name="outputFormat_selector" value="homer" />
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff changeset
375 </conditional>
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff changeset
376 </conditional>
5
ebf7f3397e79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 1
diff changeset
377 <output name="output_converted_matrix" file="hicConvertFormat/small_test_matrix_chr4.homer" ftype="zip" compare="sim_size" delta="40000" />
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff changeset
378 </test>
7
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
379 <test expect_num_outputs="1">
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
380 <conditional name="outputSingleMultiple_conditional">
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
381 <param name="outputSingleMultiple_selector" value="singleMatrix" />
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
382 <conditional name="inputFormat_conditional">
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
383 <param name="inputFormat_selector" value="optionCool" />
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
384 <param name="matrix_h5_cooler" value="hicConvertFormat/small_test_matrix_chr4.cool" />
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff changeset
385 </conditional>
1
e98b42e74a76 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
parents: 0
diff changeset
386
7
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
387 <conditional name="outputFormat_conditional">
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
388 <param name="outputFormat_selector" value="ginteractions" />
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff changeset
389 </conditional>
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff changeset
390 </conditional>
5
ebf7f3397e79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 1
diff changeset
391 <output name="output_converted_matrix" file="hicConvertFormat/small_test_matrix_chr4.ginteractions.tsv" ftype="tabular" />
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff changeset
392 </test>
7
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
393 <test expect_num_outputs="2">
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
394 <conditional name="outputSingleMultiple_conditional">
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
395 <param name="outputSingleMultiple_selector" value="singleMatrix" />
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
396 <conditional name="inputFormat_conditional">
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
397 <param name="inputFormat_selector" value="optionCool" />
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
398 <param name="matrix_h5_cooler" value="hicConvertFormat/small_test_matrix_chr4.cool" />
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
399 </conditional>
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
400
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
401 <conditional name="outputFormat_conditional">
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
402 <param name="outputFormat_selector" value="hicpro" />
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
403 </conditional>
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
404 </conditional>
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
405 <output name="output_converted_matrix" file="hicConvertFormat/small_test_matrix_chr4.hicpro" ftype="tabular" />
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
406 <output name="output_converted_matrix_bed" file="hicConvertFormat/small_test_matrix_chr4.bed" ftype="tabular" />
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
407 </test>
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
408 <test expect_num_outputs="2">
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
409 <conditional name="outputSingleMultiple_conditional">
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
410 <param name="outputSingleMultiple_selector" value="multipleMatrix" />
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
411 <conditional name="resolutionOrManyToOne_conditional">
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
412 <param name="resolutionOrManyToOne_selector" value="resolution_option" />
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
413 <param name="resolutions" value="5000 10000 20000" />
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
414 <conditional name="inputFormat_conditional">
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
415 <param name="inputFormat_selector" value="optionH5" />
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
416 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
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diff changeset
417 </conditional>
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
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diff changeset
418 </conditional>
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
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diff changeset
419 </conditional>
7
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
420 <output name="output_converted_matrix_multi" ftype="mcool">
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
parents:
diff changeset
421 <assert_contents>
7
d3dc261a47ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 6
diff changeset
422 <has_h5_keys keys="resolutions" />
0
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
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diff changeset
423 </assert_contents>
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
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diff changeset
424 </output>
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
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diff changeset
425 </test>
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
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diff changeset
426 </tests>
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
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diff changeset
427 <help><![CDATA[
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
bgruening
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428 Converting between different Hi-C interaction formats
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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429 =====================================================
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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430
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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431 Conversion of Hi-C matrices of different file formats. We support the conversion of hic to cool format via hic2cool,
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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432 and homer, HicPro, h5 and cool format to h5, cool, homer or ginteractions format. Moreover, hicConvertFormat accepts multiple input files
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433 from one format with different resolutions and creates a mcool file. Each original file is stored under a path, e.g. matrix.mcool::/resolutions/10000.
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434 A batch computation is possible, the number of input files and output files needs to match, all input files need to be of the same format type and
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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435 all output files too.
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436 For input and output of cooler files, special options are available, for all other formats they will be ignored.
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437 HiCPro file format needs an additional bed file as input.
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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438
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439 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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440
dd34ef4a5a7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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441 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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442 ]]> </help>
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443 <expand macro="citations" />
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444 </tool>