Mercurial > repos > bgruening > hicexplorer_hictransform
annotate macros.xml @ 13:dc25d1f9927b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3e5c2f8ce3e540b0474746a33ee20b4a374dd38c"
author | iuc |
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date | Fri, 11 Dec 2020 21:07:29 +0000 |
parents | b3553a0a5dcf |
children | 9667ab8e2085 |
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0
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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1 <macros> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> |
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b3553a0a5dcf
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
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3 <token name="@WRAPPER_VERSION@">3.4.3</token> |
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303558d3bc11
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@"> |
303558d3bc11
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": |
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dc25d1f9927b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3e5c2f8ce3e540b0474746a33ee20b4a374dd38c"
iuc
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6 --range $use_range.range_min:$use_range.range_max |
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303558d3bc11
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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7 #end if |
303558d3bc11
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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8 </token> |
303558d3bc11
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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369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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10 <xml name="requirements"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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11 <requirements> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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12 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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13 <yield /> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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14 </requirements> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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15 <version_command>@BINARY@ --version</version_command> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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16 </xml> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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17 |
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ae9cc6dbfaca
"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@"> |
ae9cc6dbfaca
"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: |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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20 #set $chromosomes = [] |
ae9cc6dbfaca
"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: |
ae9cc6dbfaca
"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) |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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23 #end for |
ae9cc6dbfaca
"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) |
ae9cc6dbfaca
"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 |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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26 #end if |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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27 </token> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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28 |
ae9cc6dbfaca
"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"> |
ae9cc6dbfaca
"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."> |
ae9cc6dbfaca
"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="" > |
ae9cc6dbfaca
"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" /> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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33 </param> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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34 </repeat> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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35 </xml> |
ae9cc6dbfaca
"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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369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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37 <xml name="citations"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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38 <citations> |
1
0c13bd882a1a
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 8def073a083b0619e366436a067a614555190058
iuc
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39 <citation type="doi">10.5281/zenodo.1133705</citation> |
0
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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40 <yield /> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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41 </citations> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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42 </xml> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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43 |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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44 <xml name="zMax"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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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 --> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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46 </xml> |
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303558d3bc11
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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47 <xml name="use_range"> |
303558d3bc11
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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d5bf6e7d3800
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
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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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303558d3bc11
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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50 <option value="no_use_range">No restriction</option> |
303558d3bc11
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> |
303558d3bc11
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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52 </param> |
303558d3bc11
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"/> |
303558d3bc11
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"> |
303558d3bc11
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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55 <expand macro='range' /> |
303558d3bc11
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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56 </when> |
303558d3bc11
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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57 </conditional> |
303558d3bc11
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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58 </xml> |
303558d3bc11
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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59 |
303558d3bc11
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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d5bf6e7d3800
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
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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."/> |
d5bf6e7d3800
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
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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 |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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65 <xml name="colormap"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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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"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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67 <option value="RdYlBu">RdYlBu</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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68 <option value="Accent">Accent</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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69 <option value="Spectral">Spectral</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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70 <option value="Set1">Set1</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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71 <option value="Set2">Set2</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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72 <option value="Set3">Set3</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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73 <option value="Dark2">Dark2</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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74 <option value="Reds">Reds</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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75 <option value="Oranges">Oranges</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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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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ae9cc6dbfaca
"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> |
0
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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> |
369f6cb43a86
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148 <option value="Purples_r">Purples reversed</option> |
369f6cb43a86
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149 <option value="Paired_r">Paired reversed</option> |
369f6cb43a86
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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> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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155 <option value="winter_r">winter reversed</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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156 <option value="hot_r">hot reversed</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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157 <option value="coolwarm_r">coolwarm reversed</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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158 <option value="cool_r">cool reversed</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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159 <option value="seismic_r">seismic reversed</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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160 <option value="terrain_r">terrain reversed</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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161 <option value="ocean_r">ocean reversed</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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162 <option value="rainbow_r">rainbow reversed</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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163 <option value="bone_r">bone reversed</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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164 <option value="flag_r">flag reversed</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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165 <option value="prism_r">prism reversed</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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166 <option value="cubehelix_r">cubehelix reversed</option> |
369f6cb43a86
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167 <option value="binary_r">binary reversed</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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168 <option value="pink_r">pink reversed</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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169 <option value="gray_r">gray reversed</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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170 <option value="copper_r">copper reversed</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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171 <option value="BrBG_r">BrBG reversed</option> |
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172 <option value="BuGn_r">BuGn reversed</option> |
369f6cb43a86
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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> |
369f6cb43a86
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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> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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194 <option value="gist_yarg_r">gist_yarg reversed</option> |
369f6cb43a86
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195 <option value="gist_ncar_r">gist_ncar reversed</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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196 <option value="gist_rainbow_r">gist_rainbow reversed</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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197 <option value="gist_heat_r">gist_heat reversed</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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198 <option value="gnuplot_r">gnuplot reversed</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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199 <option value="gnuplot2_r">gnuplot2 reversed</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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200 <option value="CMRmap_r">CMRmap reversed</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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201 <option value="bwr_r">bwr reversed</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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202 <option value="hsv_r">hsv reversed</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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203 <option value="brg_r">brg reversed</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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204 <option value="jet_r">jet reversed</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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205 <option value="afmhot_r">afmhot reversed</option> |
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ae9cc6dbfaca
"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> |
0
369f6cb43a86
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207 </param> |
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208 </xml> |
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209 |
369f6cb43a86
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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 |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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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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ae9cc6dbfaca
"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'; |
ae9cc6dbfaca
"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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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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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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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='hic' 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 |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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384 <when value="optionHomer"> |
ae9cc6dbfaca
"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'/> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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386 </when> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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387 |
ae9cc6dbfaca
"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"> |
ae9cc6dbfaca
"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'/> |
ae9cc6dbfaca
"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'/> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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391 </when> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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392 </conditional> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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393 </xml> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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394 |
ae9cc6dbfaca
"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'> |
ae9cc6dbfaca
"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"> |
ae9cc6dbfaca
"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"> |
ae9cc6dbfaca
"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> |
ae9cc6dbfaca
"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> |
ae9cc6dbfaca
"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> |
ae9cc6dbfaca
"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> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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402 </param> |
ae9cc6dbfaca
"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"> |
ae9cc6dbfaca
"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' /> |
ae9cc6dbfaca
"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'/> |
ae9cc6dbfaca
"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'/> |
ae9cc6dbfaca
"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'/> |
ae9cc6dbfaca
"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'/> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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409 |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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410 </when> |
ae9cc6dbfaca
"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"> |
ae9cc6dbfaca
"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' /> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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413 </when> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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414 |
ae9cc6dbfaca
"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"> |
ae9cc6dbfaca
"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"/> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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417 </when> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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418 |
ae9cc6dbfaca
"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"> |
ae9cc6dbfaca
"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"/> |
ae9cc6dbfaca
"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"/> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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422 </when> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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423 </conditional> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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424 </xml> |
ae9cc6dbfaca
"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'> |
ae9cc6dbfaca
"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> --> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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427 |
ae9cc6dbfaca
"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"> |
ae9cc6dbfaca
"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"> |
ae9cc6dbfaca
"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> |
ae9cc6dbfaca
"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> |
ae9cc6dbfaca
"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> |
ae9cc6dbfaca
"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> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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434 |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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435 </param> |
ae9cc6dbfaca
"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"> |
ae9cc6dbfaca
"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'/> |
ae9cc6dbfaca
"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'/> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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439 </when> |
ae9cc6dbfaca
"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'/> |
ae9cc6dbfaca
"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'/> |
ae9cc6dbfaca
"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'/> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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443 |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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444 </conditional> |
ae9cc6dbfaca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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445 </xml> |
0
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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446 <token name="@REFERENCES@"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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447 |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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448 .. class:: infomark |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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449 |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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450 For more information on the tools, please visit our `help site`_. |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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451 |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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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 |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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453 |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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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`_. |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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455 |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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456 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/ |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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457 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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458 .. _help site: https://hicexplorer.readthedocs.org |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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459 |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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|
460 </token> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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461 |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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462 |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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463 <xml name="multiple_input_bams"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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464 <repeat name="input_files" title="BAM files" min="2"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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465 <param name="bamfile" type="data" format="bam" |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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466 label="Bam file" |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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467 help="The BAM file must be sorted."/> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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468 <param name="label" type="text" size="30" optional="true" value="" |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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469 label="Label" |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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470 help="Label to use in the output. If not given the dataset name will be used instead."/> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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471 </repeat> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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472 </xml> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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473 |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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474 <xml name="multiple_input_bigwigs"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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475 <repeat name="input_files" title="BigWig files" min="2"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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476 <param name="bigwigfile" type="data" format="bigwig" |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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477 label="Bigwig file" |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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478 help="The Bigwig file must be sorted."/> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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479 <param name="label" type="text" size="30" optional="true" value="" |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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480 label="Label" |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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481 help="Label to use in the output. If not given the dataset name will be used instead."/> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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482 </repeat> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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483 </xml> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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484 |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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485 <xml name="plotTitle"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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486 <param name="plotTitle" type="text" value="" size="30" optional="True" |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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487 label="Title of the plot" |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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488 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" /> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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489 </xml> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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490 |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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491 <token name="@multiple_input_bams@"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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492 #import tempfile |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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493 #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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494 #set files=[] |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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495 #set labels=[] |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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496 #for $i in $input_files: |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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497 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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498 #set $temp_input_path = $temp_input_handle.name |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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499 #silent $temp_input_handle.close() |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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500 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path)) |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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501 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path)) |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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502 #silent $files.append('%s.bam' % $temp_input_path) |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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503 |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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504 ##set $files += [str($i.bamfile)] |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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505 #if str($i.label.value) != "": |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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506 #set $labels += ["\"%s\"" % ($i.label.value)] |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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507 #else |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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508 #set $labels += ["\"%s\"" % ($i.bamfile.name)] |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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509 #end if |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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510 #end for |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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511 </token> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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512 |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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513 <token name="@multiple_input_bigwigs@"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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514 #import tempfile |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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515 #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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516 #set files=[] |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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517 #set labels=[] |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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518 #for $i in $input_files: |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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519 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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520 #set $temp_input_path = $temp_input_handle.name |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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521 #silent $temp_input_handle.close() |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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522 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path)) |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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523 #silent $files.append('%s.bw' % $temp_input_path) |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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524 |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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525 ##set $files += [str($i.bigwigfile)] |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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526 #if str($i.label.value) != "": |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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527 #set $labels += ["\"%s\"" % ($i.label.value)] |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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528 #else |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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529 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)] |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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530 #end if |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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531 #end for |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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532 </token> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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533 |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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534 <xml name="reference_genome_source"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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535 <conditional name="source"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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536 <param name="ref_source" type="select" label="Reference genome"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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537 <option value="cached">locally cached</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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538 <option value="history">in your history</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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539 </param> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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540 <when value="cached"> |
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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"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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620 <param name="outFileFormat" type="select" label="Image file format"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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621 <option value="png" selected="true">png</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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622 <option value="pdf">pdf</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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623 <option value="svg">svg</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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624 <option value="eps">eps</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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625 <option value="emf">emf</option> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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626 </param> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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627 </xml> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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628 |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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629 <xml name="output_image_file_format"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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630 <data format="png" name="outFileName" label="${tool.name} image"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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631 <change_format> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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632 <when input="output.outFileFormat" value="pdf" format="pdf" /> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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633 <when input="output.outFileFormat" value="svg" format="svg" /> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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634 <when input="output.outFileFormat" value="eps" format="eps" /> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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635 <when input="output.outFileFormat" value="emf" format="emf" /> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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636 </change_format> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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637 </data> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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638 </xml> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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639 |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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640 <xml name="output_save_matrix_values"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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641 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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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 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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643 (( |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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644 output['showOutputSettings'] == 'yes' and |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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645 output['saveMatrix'] is True |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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646 )) |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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647 </filter> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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648 </data> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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649 </xml> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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650 |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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651 <xml name="output_graphic_outputs"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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652 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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|
653 <filter> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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654 (( |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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655 output['showOutputSettings'] == 'yes' and |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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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 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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657 )) |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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|
658 </filter> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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659 </data> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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660 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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661 <filter> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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662 (( |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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663 output['showOutputSettings'] == 'yes' and |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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664 output['saveSortedRegions'] is True |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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665 )) |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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666 </filter> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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667 </data> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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668 </xml> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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669 |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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670 <xml name="track_input_h5_macro"> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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671 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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672 </xml> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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673 <xml name="track_input_bed_macro"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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674 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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675 </xml> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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676 <xml name="track_input_bedgraph_macro"> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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677 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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678 </xml> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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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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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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681 </xml> |
369f6cb43a86
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682 <xml name="track_input_bedgraph_matrix_macro"> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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683 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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684 </xml> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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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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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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687 </xml> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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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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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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690 </xml> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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691 |
369f6cb43a86
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692 <xml name="spacer_macro"> |
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693 <param name="spacer_width" type="float" value="" optional="True" |
3
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694 label="Include spacer at the end of the track." help="Width of the spacer." /> |
0
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695 </xml> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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696 <xml name="fontsize_macro"> |
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697 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> |
0
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698 </xml> |
369f6cb43a86
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
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699 </macros> |