Mercurial > repos > bgruening > hicexplorer_hiccorrelate
annotate macros.xml @ 12:e89d515c3594 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
author | bgruening |
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date | Mon, 16 Dec 2019 15:39:31 -0500 |
parents | 8a5b13451a9e |
children | 5fe7376d9ff0 |
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fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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1 <macros> |
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ae2d7e2dfeef
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> |
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e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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3 <token name="@WRAPPER_VERSION@">3.3.1</token> |
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602a0c6f4bb0
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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4 <token name="@USE_RANGE@"> |
602a0c6f4bb0
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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5 #if $use_range.select_use_range == "yes_use_range": |
602a0c6f4bb0
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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6 --range $range_min:$range_max |
602a0c6f4bb0
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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7 #end if |
602a0c6f4bb0
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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8 </token> |
602a0c6f4bb0
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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9 |
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fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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10 <xml name="requirements"> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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11 <requirements> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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12 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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13 <yield /> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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14 </requirements> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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15 <version_command>@BINARY@ --version</version_command> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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16 </xml> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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17 |
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e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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18 <token name="@CHROMOSOME_LIST@"> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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19 #if $chromosome_list: |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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20 #set $chromosomes = [] |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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21 #for $chrom in $chromosome_list: |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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22 #silent $chromosomes.append("'%s'" % $chrom.chromosomes) |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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23 #end for |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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24 #set $chromosome_string = ' '.join($chromosomes) |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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25 --chromosomes $chromosome_string |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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26 #end if |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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27 </token> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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28 |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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29 <xml name="chromosome_list"> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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30 <repeat name="chromosome_list" min="0" title="Chromosomes to include" help="Chromosomes to include in the analysis. If not set, all chromosomes are included."> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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31 <param argument="--chromosomes" type="text" value="" > |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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32 <validator type="empty_field" /> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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33 </param> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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34 </repeat> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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35 </xml> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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36 |
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fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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37 <xml name="citations"> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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38 <citations> |
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8187f841afea
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 8def073a083b0619e366436a067a614555190058
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39 <citation type="doi">10.5281/zenodo.1133705</citation> |
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fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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40 <yield /> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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41 </citations> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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42 </xml> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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43 |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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44 <xml name="zMax"> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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45 <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow --> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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46 </xml> |
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602a0c6f4bb0
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47 <xml name="use_range"> |
602a0c6f4bb0
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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48 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range --> |
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49 <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range" help="If given, only counts within the specified range are considered."> |
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50 <option value="no_use_range">No restriction</option> |
602a0c6f4bb0
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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51 <option value="yes_use_range">Only consider counts within a range</option> |
602a0c6f4bb0
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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52 </param> |
602a0c6f4bb0
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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53 <when value="no_use_range"/> |
602a0c6f4bb0
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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54 <when value="yes_use_range"> |
602a0c6f4bb0
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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55 <expand macro='range' /> |
602a0c6f4bb0
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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56 </when> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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57 </conditional> |
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58 </xml> |
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59 |
602a0c6f4bb0
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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60 <xml name="range"> |
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61 <param name='range_min' label="Minimum range to consider interactions" type="integer" value="" min="0" help="The minimum range should be farer from the diagonal than median TAD size in order to reduce background interactions."/> |
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62 <param name='range_max' label="Maximum range to consider interactions" type="integer" value="" min="0"/> |
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63 </xml> |
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64 |
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65 <xml name="colormap"> |
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66 <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> |
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67 <option value="RdYlBu">RdYlBu</option> |
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68 <option value="Accent">Accent</option> |
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69 <option value="Spectral">Spectral</option> |
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70 <option value="Set1">Set1</option> |
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71 <option value="Set2">Set2</option> |
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72 <option value="Set3">Set3</option> |
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73 <option value="Dark2">Dark2</option> |
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74 <option value="Reds">Reds</option> |
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75 <option value="Oranges">Oranges</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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76 <option value="Greens">Greens</option> |
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77 <option value="Blues">Blues</option> |
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78 <option value="Greys">Greys</option> |
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79 <option value="Purples">Purples</option> |
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80 <option value="Paired">Paired</option> |
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81 <option value="Pastel1">Pastel1</option> |
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82 <option value="Pastel2">Pastel2</option> |
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83 <option value="spring">spring</option> |
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84 <option value="summer">summer</option> |
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85 <option value="autumn">autumn</option> |
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86 <option value="winter">winter</option> |
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87 <option value="hot">hot</option> |
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88 <option value="coolwarm">coolwarm</option> |
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89 <option value="cool">cool</option> |
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90 <option value="seismic">seismic</option> |
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91 <option value="terrain">terrain</option> |
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92 <option value="ocean">ocean</option> |
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93 <option value="rainbow">rainbow</option> |
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94 <option value="bone">bone</option> |
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95 <option value="flag">flag</option> |
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96 <option value="prism">prism</option> |
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97 <option value="cubehelix">cubehelix</option> |
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98 <option value="binary">binary</option> |
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99 <option value="pink">pink</option> |
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100 <option value="gray">gray</option> |
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101 <option value="copper">copper</option> |
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102 <option value="BrBG">BrBG</option> |
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103 <option value="BuGn">BuGn</option> |
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104 <option value="BuPu">BuPu</option> |
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105 <option value="GnBu">GnBu</option> |
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106 <option value="OrRd">OrRd</option> |
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107 <option value="PiYG">PiYG</option> |
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108 <option value="PRGn">PRGn</option> |
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109 <option value="PuOr">PuOr</option> |
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110 <option value="PuRd">PuRd</option> |
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111 <option value="PuBu">PuBu</option> |
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112 <option value="RdBu">RdBu</option> |
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113 <option value="RdGy">RdGy</option> |
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114 <option value="RdPu">RdPu</option> |
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115 <option value="YlGn">YlGn</option> |
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116 <option value="PuBuGn">PuBuGn</option> |
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117 <option value="RdYlGn">RdYlGn</option> |
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118 <option value="YlGnBu">YlGnBu</option> |
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119 <option value="YlOrBr">YlOrBr</option> |
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120 <option value="YlOrRd">YlOrRd</option> |
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121 <option value="gist_gray">gist_gray</option> |
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122 <option value="gist_stern">gist_stern</option> |
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123 <option value="gist_earth">gist_earth</option> |
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124 <option value="gist_yarg">gist_yarg</option> |
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125 <option value="gist_ncar">gist_ncar</option> |
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126 <option value="gist_rainbow">gist_rainbow</option> |
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127 <option value="gist_heat">gist_heat</option> |
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128 <option value="gnuplot">gnuplot</option> |
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129 <option value="gnuplot2">gnuplot2</option> |
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130 <option value="CMRmap">CMRmap</option> |
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131 <option value="bwr">bwr</option> |
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132 <option value="hsv">hsv</option> |
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133 <option value="brg">brg</option> |
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134 <option value="jet">jet</option> |
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135 <option value="afmhot">afmhot</option> |
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e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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136 <option value="plasma">plasma</option> |
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137 <option value="Accent_r">Accent reversed</option> |
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138 <option value="Spectral_r">Spectral reversed</option> |
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139 <option value="Set1_r">Set1 reversed</option> |
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140 <option value="Set2_r">Set2 reversed</option> |
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141 <option value="Set3_r">Set3 reversed</option> |
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142 <option value="Dark2_r">Dark2 reversed</option> |
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143 <option value="Reds_r">Reds reversed</option> |
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144 <option value="Oranges_r">Oranges reversed</option> |
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145 <option value="Greens_r">Greens reversed</option> |
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146 <option value="Blues_r">Blues reversed</option> |
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147 <option value="Greys_r">Greys reversed</option> |
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148 <option value="Purples_r">Purples reversed</option> |
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149 <option value="Paired_r">Paired reversed</option> |
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150 <option value="Pastel1_r">Pastel1 reversed</option> |
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151 <option value="Pastel2_r">Pastel2 reversed</option> |
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152 <option value="spring_r">spring reversed</option> |
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153 <option value="summer_r">summer reversed</option> |
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154 <option value="autumn_r">autumn reversed</option> |
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155 <option value="winter_r">winter reversed</option> |
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156 <option value="hot_r">hot reversed</option> |
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157 <option value="coolwarm_r">coolwarm reversed</option> |
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158 <option value="cool_r">cool reversed</option> |
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159 <option value="seismic_r">seismic reversed</option> |
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160 <option value="terrain_r">terrain reversed</option> |
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161 <option value="ocean_r">ocean reversed</option> |
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162 <option value="rainbow_r">rainbow reversed</option> |
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163 <option value="bone_r">bone reversed</option> |
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164 <option value="flag_r">flag reversed</option> |
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165 <option value="prism_r">prism reversed</option> |
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166 <option value="cubehelix_r">cubehelix reversed</option> |
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167 <option value="binary_r">binary reversed</option> |
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168 <option value="pink_r">pink reversed</option> |
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169 <option value="gray_r">gray reversed</option> |
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170 <option value="copper_r">copper reversed</option> |
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171 <option value="BrBG_r">BrBG reversed</option> |
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172 <option value="BuGn_r">BuGn reversed</option> |
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173 <option value="BuPu_r">BuPu reversed</option> |
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174 <option value="GnBu_r">GnBu reversed</option> |
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175 <option value="OrRd_r">OrRd reversed</option> |
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176 <option value="PiYG_r">PiYG reversed</option> |
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177 <option value="PRGn_r">PRGn reversed</option> |
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178 <option value="PuOr_r">PuOr reversed</option> |
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179 <option value="PuRd_r">PuRd reversed</option> |
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180 <option value="PuBu_r">PuBu reversed</option> |
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181 <option value="RdBu_r">RdBu reversed</option> |
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182 <option value="RdGy_r">RdGy reversed</option> |
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183 <option value="RdPu_r">RdPu reversed</option> |
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184 <option value="YlGn_r">YlGn reversed</option> |
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185 <option value="PuBuGn_r">PuBuGn reversed</option> |
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186 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option> |
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187 <option value="RdYlGn_r">RdYlGn reversed</option> |
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188 <option value="YlGnBu_r">YlGnBu reversed</option> |
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189 <option value="YlOrBr_r">YlOrBr reversed</option> |
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190 <option value="YlOrRd_r">YlOrRd reversed</option> |
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191 <option value="gist_gray_r">gist_gray reversed</option> |
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192 <option value="gist_stern_r">gist_stern reversed</option> |
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193 <option value="gist_earth_r">gist_earth reversed</option> |
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194 <option value="gist_yarg_r">gist_yarg reversed</option> |
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195 <option value="gist_ncar_r">gist_ncar reversed</option> |
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196 <option value="gist_rainbow_r">gist_rainbow reversed</option> |
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197 <option value="gist_heat_r">gist_heat reversed</option> |
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198 <option value="gnuplot_r">gnuplot reversed</option> |
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199 <option value="gnuplot2_r">gnuplot2 reversed</option> |
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200 <option value="CMRmap_r">CMRmap reversed</option> |
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201 <option value="bwr_r">bwr reversed</option> |
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202 <option value="hsv_r">hsv reversed</option> |
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203 <option value="brg_r">brg reversed</option> |
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204 <option value="jet_r">jet reversed</option> |
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205 <option value="afmhot_r">afmhot reversed</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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206 <option value="plasma_r">plasma reversed</option> |
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207 </param> |
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208 </xml> |
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209 |
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210 <xml name="multiple_input_matrices"> |
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211 <repeat name="input_files" title="Hi-C Matrix files" min="2"> |
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212 <param name="matrix" type="data" format="h5,cool" |
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213 label="Hi-C Matrix file" |
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214 help=""/> |
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215 <param name="mlabel" type="text" size="30" optional="true" value="" |
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216 label="Label" |
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217 help="Label to use in the output. If not given the dataset name will be used instead."/> |
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218 </repeat> |
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219 </xml> |
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220 |
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221 <token name="@multiple_input_matrices@"> |
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222 #set $matrices = [] |
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223 #set $mlabels = [] |
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224 #for $counter, $i in enumerate($input_files): |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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225 ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext'; |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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226 #silent $matrices.append( '\'%s_matrix.%s\'' % ($counter, $i.matrix.ext)) |
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227 |
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228 #if str($i.mlabel.value) != "": |
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229 #set $mlabels += ['\'%s\'' % ($i.mlabel.value)] |
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230 #else |
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231 #set $mlabels += ['\'%s\'' % ($i.matrix.name)] |
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232 #end if |
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233 #end for |
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234 #set $mlabels = ' '.join($mlabels) |
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235 #set $matrices = ' '.join($matrices) |
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236 </token> |
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237 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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238 <token name="@ESCAPE_IDENTIFIER_FILE@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($file.element_identifier))]]></token> |
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239 <token name="@ESCAPE_IDENTIFIER_MATRIX@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($matrix.element_identifier))]]></token> |
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240 <token name="@ESCAPE_IDENTIFIER_M@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($m.element_identifier))]]></token> |
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241 |
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242 <xml name="region"> |
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243 <param name="region" type="text" label="Region of the genome to limit the operation" |
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244 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" argument="--region"/> |
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245 </xml> |
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246 |
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247 |
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248 |
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249 <xml name="kmeans_clustering"> |
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250 <conditional name="used_multiple_regions"> |
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251 <param name="used_multiple_regions_options" type="select" |
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252 label="Did you compute the matrix with more than one groups of regions?" |
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253 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions."> |
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254 <option value="yes">Yes, I used multiple groups of regions</option> |
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255 <option value="no">No, I used only one group</option> |
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256 </param> |
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257 <when value="no"> |
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258 <conditional name="clustering"> |
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259 <param name="clustering_options" type="select" label="Clustering algorithm"> |
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260 <option value="none">No clustering</option> |
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261 <option value="kmeans">Kmeans clustering</option> |
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262 </param> |
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263 <when value="kmeans"> |
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264 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" |
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265 help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/> |
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266 </when> |
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267 <when value="none" /> |
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268 </conditional> |
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269 </when> |
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270 <when value="yes" /> |
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271 </conditional> |
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272 </xml> |
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273 |
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274 <token name="@KMEANS_CLUSTERING@"> |
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275 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': |
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276 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': |
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277 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: |
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278 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans |
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279 #end if |
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280 #end if |
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281 #end if |
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282 </token> |
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283 |
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284 <xml name="samFlag"> |
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285 <param name="samFlag" type="integer" optional="true" value="" |
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286 label="Filter reads based on the SAM flag" |
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287 help= "For example to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage. (--samFlag)"/> |
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288 </xml> |
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289 <xml name="plotNumbers"> |
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290 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" |
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291 label="Plot the correlation value" |
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292 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/> |
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293 </xml> |
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294 <xml name="doNotExtendPairedEnds"> |
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295 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" |
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296 label="Do not extend paired ends" |
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297 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available. (--doNotExtendPairedEnds)"/> |
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298 </xml> |
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299 |
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300 <xml name="ignoreDuplicates"> |
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301 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" |
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302 label="Ignore duplicates" |
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303 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read. (--ignoreDuplicates)" /> |
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304 </xml> |
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305 |
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306 <xml name="minMappingQuality"> |
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307 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1" |
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308 label="Minimum mapping quality" |
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309 help= "If set, only reads that have a mapping quality score higher than the given value are considered. |
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310 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. |
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311 A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/> |
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312 </xml> |
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313 |
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314 <xml name="skipZeros"> |
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315 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" |
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316 label ="Skip zeros" |
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317 help ="If set, then zero counts that happen for *all* BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined. (--skipZeros)" /> |
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318 </xml> |
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319 |
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320 <xml name="fragmentLength"> |
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321 <param name="fragmentLength" type="integer" value="300" min="1" |
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322 label="Fragment length used for the sequencing" |
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323 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/> |
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324 </xml> |
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325 |
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326 <xml name="scaleFactor"> |
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327 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/> |
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328 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/> |
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329 </xml> |
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330 |
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331 <xml name="xMax"> |
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332 <param argument="--xMax" name="xMax" type="integer" optional="true" value="" |
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333 label="Max value for the x-axis in counts per bin" /> |
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334 </xml> |
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335 |
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336 <xml name="filterThreshold"> |
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337 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5" |
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338 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/> |
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339 |
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340 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0" |
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341 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/> |
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342 </xml> |
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343 |
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344 |
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345 <xml name="pseudocount"> |
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346 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/> |
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347 </xml> |
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348 <xml name='matrix_h5_cooler_macro'> |
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349 <param name='matrix_h5_cooler' type="data" format="h5,cool" |
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350 label="Matrix to compute on"/> |
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351 </xml> |
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352 <xml name='matrix_h5_cooler_multiple_macro'> |
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353 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" |
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354 label="Matricies to compute on" multiple="true"/> |
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355 </xml> |
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356 |
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357 |
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358 |
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359 <xml name='convertFormat_single_macro'> |
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360 <conditional name="inputFormat_conditional"> |
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361 <param name="inputFormat_selector" type="select" label="Choose input file type"> |
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362 <option value="optionCool" selected="True">cool</option> |
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363 <option value="optionH5">h5</option> |
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364 <!-- <option value="optionHic">hic</option> --> |
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365 <option value="optionHomer">Homer</option> |
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366 <option value="optionHicpro">HiCPro</option> |
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367 </param> |
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368 <when value="optionCool"> |
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369 <expand macro='matrix_h5_cooler_macro' /> |
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370 <param name='correctionName' type='text' label='Correction factors column name'/> |
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371 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication'/> |
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372 <param name='chromosome' type='text' label='Load only one chromosome'/> |
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373 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data'/> |
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374 |
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375 </when> |
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376 <when value="optionH5"> |
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377 <expand macro='matrix_h5_cooler_macro' /> |
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378 </when> |
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379 <!-- <when value="optionHic"> |
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380 <param name='matrixHic' type='data' format='binary' label='.hic matrix'/> |
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381 <param name='resolutions' type='text' label='List of resolutions'/> |
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382 </when> --> |
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383 |
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384 <when value="optionHomer"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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385 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix'/> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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386 </when> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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387 |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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388 <when value="optionHicpro"> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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389 <param name='matrixHicpro' type='data' format='txt' label='.hic matrix'/> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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390 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file'/> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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391 </when> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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392 </conditional> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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393 </xml> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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394 |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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395 <xml name='convertFormat_multiple_macro'> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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396 <conditional name="inputFormat_conditional"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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397 <param name="inputFormat_selector" type="select" label="Choose input file type"> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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398 <option value="optionCool" selected="True">cool</option> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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399 <option value="optionH5">h5</option> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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400 <option value="optionHomer">Homer</option> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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401 <option value="optionHicpro">HiCPro</option> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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402 </param> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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403 <when value="optionCool"> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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404 <expand macro='matrix_h5_cooler_multiple_macro' /> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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405 <param name='correctionName' type='text' label='Correction factors column name'/> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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406 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication'/> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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407 <param name='chromosome' type='text' label='Load only one chromosome'/> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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408 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data'/> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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409 |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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410 </when> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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411 <when value="optionH5"> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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412 <expand macro='matrix_h5_cooler_multiple_macro' /> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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413 </when> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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414 |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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415 <when value="optionHomer"> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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416 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' multiple="true"/> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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417 </when> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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418 |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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419 <when value="optionHicpro"> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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420 <param name='matrixHicpro' type='data' format='txt' label='.hic matrix' multiple="true"/> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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421 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' multiple="true"/> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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422 </when> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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423 </conditional> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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424 </xml> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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425 <xml name='convertFormat_single_output_macro'> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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426 <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> --> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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427 |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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428 <conditional name="outputFormat_conditional"> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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429 <param name="outputFormat_selector" type="select" label="Choose output file type"> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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430 <option value="cool" selected="True">cool</option> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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431 <option value="h5">h5</option> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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432 <option value="homer">Homer</option> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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433 <option value="ginteractions">ginteractions</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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434 |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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435 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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436 <when value="cool"> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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437 <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count'/> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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438 <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column'/> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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439 </when> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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440 <when value='h5'/> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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441 <when value='homer'/> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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442 <when value='ginteractions'/> |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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443 |
e89d515c3594
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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444 </conditional> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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445 </xml> |
0
fe0243c46b36
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446 <token name="@REFERENCES@"> |
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447 |
fe0243c46b36
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448 .. class:: infomark |
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449 |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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450 For more information on the tools, please visit our `help site`_. |
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451 |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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452 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com |
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453 |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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454 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. |
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455 |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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456 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/ |
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457 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de |
2
ae2d7e2dfeef
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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458 .. _help site: https://hicexplorer.readthedocs.org |
0
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459 |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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460 </token> |
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461 |
fe0243c46b36
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|
462 |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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463 <xml name="multiple_input_bams"> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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464 <repeat name="input_files" title="BAM files" min="2"> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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465 <param name="bamfile" type="data" format="bam" |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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466 label="Bam file" |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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467 help="The BAM file must be sorted."/> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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468 <param name="label" type="text" size="30" optional="true" value="" |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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469 label="Label" |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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470 help="Label to use in the output. If not given the dataset name will be used instead."/> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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471 </repeat> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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472 </xml> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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473 |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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474 <xml name="multiple_input_bigwigs"> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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475 <repeat name="input_files" title="BigWig files" min="2"> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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476 <param name="bigwigfile" type="data" format="bigwig" |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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477 label="Bigwig file" |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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478 help="The Bigwig file must be sorted."/> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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479 <param name="label" type="text" size="30" optional="true" value="" |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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480 label="Label" |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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481 help="Label to use in the output. If not given the dataset name will be used instead."/> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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482 </repeat> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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483 </xml> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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484 |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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485 <xml name="plotTitle"> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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486 <param name="plotTitle" type="text" value="" size="30" optional="True" |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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487 label="Title of the plot" |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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488 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" /> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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489 </xml> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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490 |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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491 <token name="@multiple_input_bams@"> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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492 #import tempfile |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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493 #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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494 #set files=[] |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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495 #set labels=[] |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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496 #for $i in $input_files: |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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497 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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498 #set $temp_input_path = $temp_input_handle.name |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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499 #silent $temp_input_handle.close() |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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500 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path)) |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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501 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path)) |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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502 #silent $files.append('%s.bam' % $temp_input_path) |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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503 |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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504 ##set $files += [str($i.bamfile)] |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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505 #if str($i.label.value) != "": |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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506 #set $labels += ["\"%s\"" % ($i.label.value)] |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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507 #else |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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508 #set $labels += ["\"%s\"" % ($i.bamfile.name)] |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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509 #end if |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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510 #end for |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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511 </token> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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512 |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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513 <token name="@multiple_input_bigwigs@"> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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514 #import tempfile |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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515 #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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516 #set files=[] |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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517 #set labels=[] |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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518 #for $i in $input_files: |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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519 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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520 #set $temp_input_path = $temp_input_handle.name |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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521 #silent $temp_input_handle.close() |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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522 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path)) |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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523 #silent $files.append('%s.bw' % $temp_input_path) |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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524 |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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525 ##set $files += [str($i.bigwigfile)] |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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526 #if str($i.label.value) != "": |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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527 #set $labels += ["\"%s\"" % ($i.label.value)] |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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528 #else |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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529 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)] |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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530 #end if |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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531 #end for |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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532 </token> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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533 |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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534 <xml name="reference_genome_source"> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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535 <conditional name="source"> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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536 <param name="ref_source" type="select" label="Reference genome"> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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537 <option value="cached">locally cached</option> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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538 <option value="history">in your history</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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539 </param> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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540 <when value="cached"> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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541 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> |
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542 <options from_data_table="deepTools_seqs"> |
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543 <filter type="sort_by" column="1" /> |
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544 <validator type="no_options" message="No indexes are available." /> |
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545 </options> |
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546 </param> |
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547 </when> |
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548 <when value="history"> |
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549 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" /> |
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550 </when> |
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551 </conditional> |
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552 </xml> |
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553 |
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554 <token name="@reference_genome_source@"> |
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555 #if $source.ref_source=="history": |
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556 --genome $source.input1 |
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557 #else: |
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558 --genome "${source.input1_2bit.fields.path}" |
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559 #end if |
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560 </token> |
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561 |
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562 <xml name="effectiveGenomeSize"> |
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563 <conditional name="effectiveGenomeSize"> |
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564 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" |
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565 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. |
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566 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. |
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567 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes."> |
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568 <option value="93260000">ce10 (93260000)</option> |
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569 <option value="121400000">dm3 (121400000)</option> |
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570 <option value="2451960000" selected="true">hg19 (2451960000)</option> |
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571 <option value="2150570000">mm9 (2150570000)</option> |
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572 <option value="specific">user specified</option> |
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573 </param> |
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574 <when value="specific"> |
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575 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/> |
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576 </when> |
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577 <when value="2150570000" /> |
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578 <when value="2451960000" /> |
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579 <when value="121400000" /> |
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580 <when value="93260000" /> |
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581 </conditional> |
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582 </xml> |
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583 |
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584 <xml name="image_file_format"> |
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585 <param name="outFileFormat" type="select" label="Image file format"> |
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586 <option value="png" selected="true">png</option> |
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587 <option value="pdf">pdf</option> |
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588 <option value="svg">svg</option> |
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589 <option value="eps">eps</option> |
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590 <option value="emf">emf</option> |
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591 </param> |
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592 </xml> |
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593 |
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594 <xml name="missingDataAsZero"> |
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595 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True" |
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596 label ="Treat missing data as zero" |
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597 help ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." /> |
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598 </xml> |
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599 |
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600 <xml name="input_save_matrix_values"> |
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601 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/> |
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602 </xml> |
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603 |
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604 <xml name="input_graphic_output_settings"> |
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605 <conditional name="output" > |
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606 <param name="showOutputSettings" type="select" label="Show advanced output settings" > |
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607 <option value="no" selected="true">no</option> |
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608 <option value="yes">yes</option> |
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609 </param> |
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610 <when value="no" /> |
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611 <when value="yes"> |
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612 <yield /> |
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613 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/> |
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614 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/> |
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615 </when> |
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616 </conditional> |
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617 </xml> |
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618 |
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619 <xml name="input_image_file_format"> |
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|
620 <param name="outFileFormat" type="select" label="Image file format"> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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621 <option value="png" selected="true">png</option> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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622 <option value="pdf">pdf</option> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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623 <option value="svg">svg</option> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
624 <option value="eps">eps</option> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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625 <option value="emf">emf</option> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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626 </param> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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627 </xml> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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628 |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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629 <xml name="output_image_file_format"> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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630 <data format="png" name="outFileName" label="${tool.name} image"> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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631 <change_format> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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632 <when input="output.outFileFormat" value="pdf" format="pdf" /> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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633 <when input="output.outFileFormat" value="svg" format="svg" /> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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634 <when input="output.outFileFormat" value="eps" format="eps" /> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
635 <when input="output.outFileFormat" value="emf" format="emf" /> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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636 </change_format> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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637 </data> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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638 </xml> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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639 |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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640 <xml name="output_save_matrix_values"> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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641 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values"> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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642 <filter> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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643 (( |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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644 output['showOutputSettings'] == 'yes' and |
fe0243c46b36
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645 output['saveMatrix'] is True |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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646 )) |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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647 </filter> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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648 </data> |
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649 </xml> |
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650 |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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651 <xml name="output_graphic_outputs"> |
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652 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column"> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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653 <filter> |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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654 (( |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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655 output['showOutputSettings'] == 'yes' and |
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656 output['saveData'] is True |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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657 )) |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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658 </filter> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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659 </data> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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660 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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661 <filter> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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662 (( |
fe0243c46b36
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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663 output['showOutputSettings'] == 'yes' and |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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664 output['saveSortedRegions'] is True |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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665 )) |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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666 </filter> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
667 </data> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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668 </xml> |
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669 |
2
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670 <xml name="track_input_h5_macro"> |
5
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671 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/> |
2
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672 </xml> |
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673 <xml name="track_input_bed_macro"> |
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674 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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675 </xml> |
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676 <xml name="track_input_bedgraph_macro"> |
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677 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/> |
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678 </xml> |
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679 <xml name="track_input_bigwig_macro"> |
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680 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/> |
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681 </xml> |
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682 <xml name="track_input_bedgraph_matrix_macro"> |
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683 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/> |
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684 </xml> |
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685 <xml name="track_input_tabular_macro"> |
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686 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/> |
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687 </xml> |
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688 <xml name="plot_title"> |
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689 <param name="title" type="text" optional="true" label="Plot title"/> |
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690 </xml> |
0
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691 |
2
ae2d7e2dfeef
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692 <xml name="spacer_macro"> |
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693 <param name="spacer_width" type="float" value="" optional="True" |
7
602a0c6f4bb0
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694 label="Include spacer at the end of the track." help="Width of the spacer." /> |
2
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695 </xml> |
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696 <xml name="fontsize_macro"> |
7
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697 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> |
2
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698 </xml> |
0
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699 </macros> |