Mercurial > repos > bgruening > hicexplorer_hicplottads

annotate macros.xml.orig @ 7:94fff1a6a899 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
author bgruening
date Wed, 07 Mar 2018 03:46:02 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
1 <macros>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
3 <<<<<<< HEAD
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
4 <token name="@WRAPPER_VERSION@">2.0</token>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
5
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
6 <token name="@USE_RANGE@">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
7 #if $use_range.select_use_range == "yes_use_range":
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
8 --range $range_min:$range_max
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
9 #end if
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
10 </token>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
11
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
12 =======
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
13 <token name="@WRAPPER_VERSION@">2.1alpha1</token>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
14 >>>>>>> joachimwolff-master
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
15 <xml name="requirements">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
16 <requirements>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
17 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
18 <yield />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
19 </requirements>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
20 <version_command>@BINARY@ --version</version_command>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
21 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
22
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
23 <xml name="citations">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
24 <citations>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
25 <citation type="doi">10.5281/zenodo.1133705</citation>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
26 <yield />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
27 </citations>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
28 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
29
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
30 <xml name="zMax">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
31 <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 -->
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
32 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
33 <xml name="use_range">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
34 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
35 <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
36 <option value="no_use_range">No restriction</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
37 <option value="yes_use_range">Only consider counts within a range</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
38 </param>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
39 <when value="no_use_range"/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
40 <when value="yes_use_range">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
41 <param name="range_min" type="integer" value="" min="0"/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
42 <param name="range_max" type="integer" value="" min="0"/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
43 </when>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
44 </conditional>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
45 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
46 <xml name="colormap">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
47 <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">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
48 <option value="RdYlBu">RdYlBu</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
49 <option value="Accent">Accent</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
50 <option value="Spectral">Spectral</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
51 <option value="Set1">Set1</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
52 <option value="Set2">Set2</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
53 <option value="Set3">Set3</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
54 <option value="Dark2">Dark2</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
55 <option value="Reds">Reds</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
56 <option value="Oranges">Oranges</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
57 <option value="Greens">Greens</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
58 <option value="Blues">Blues</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
59 <option value="Greys">Greys</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
60 <option value="Purples">Purples</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
61 <option value="Paired">Paired</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
62 <option value="Pastel1">Pastel1</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
63 <option value="Pastel2">Pastel2</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
64 <option value="spring">spring</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
65 <option value="summer">summer</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
66 <option value="autumn">autumn</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
67 <option value="winter">winter</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
68 <option value="hot">hot</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
69 <option value="coolwarm">coolwarm</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
70 <option value="cool">cool</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
71 <option value="seismic">seismic</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
72 <option value="terrain">terrain</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
73 <option value="ocean">ocean</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
74 <option value="rainbow">rainbow</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
75 <option value="bone">bone</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
76 <option value="flag">flag</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
77 <option value="prism">prism</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
78 <option value="cubehelix">cubehelix</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
79 <option value="binary">binary</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
80 <option value="pink">pink</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
81 <option value="gray">gray</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
82 <option value="copper">copper</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
83 <option value="BrBG">BrBG</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
84 <option value="BuGn">BuGn</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
85 <option value="BuPu">BuPu</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
86 <option value="GnBu">GnBu</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
87 <option value="OrRd">OrRd</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
88 <option value="PiYG">PiYG</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
89 <option value="PRGn">PRGn</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
90 <option value="PuOr">PuOr</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
91 <option value="PuRd">PuRd</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
92 <option value="PuBu">PuBu</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
93 <option value="RdBu">RdBu</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
94 <option value="RdGy">RdGy</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
95 <option value="RdPu">RdPu</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
96 <option value="YlGn">YlGn</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
97 <option value="PuBuGn">PuBuGn</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
98 <option value="RdYlGn">RdYlGn</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
99 <option value="YlGnBu">YlGnBu</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
100 <option value="YlOrBr">YlOrBr</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
101 <option value="YlOrRd">YlOrRd</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
102 <option value="gist_gray">gist_gray</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
103 <option value="gist_stern">gist_stern</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
104 <option value="gist_earth">gist_earth</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
105 <option value="gist_yarg">gist_yarg</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
106 <option value="gist_ncar">gist_ncar</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
107 <option value="gist_rainbow">gist_rainbow</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
108 <option value="gist_heat">gist_heat</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
109 <option value="gnuplot">gnuplot</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
110 <option value="gnuplot2">gnuplot2</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
111 <option value="CMRmap">CMRmap</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
112 <option value="bwr">bwr</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
113 <option value="hsv">hsv</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
114 <option value="brg">brg</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
115 <option value="jet">jet</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
116 <option value="afmhot">afmhot</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
117 <option value="Accent_r">Accent reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
118 <option value="Spectral_r">Spectral reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
119 <option value="Set1_r">Set1 reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
120 <option value="Set2_r">Set2 reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
121 <option value="Set3_r">Set3 reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
122 <option value="Dark2_r">Dark2 reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
123 <option value="Reds_r">Reds reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
124 <option value="Oranges_r">Oranges reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
125 <option value="Greens_r">Greens reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
126 <option value="Blues_r">Blues reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
127 <option value="Greys_r">Greys reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
128 <option value="Purples_r">Purples reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
129 <option value="Paired_r">Paired reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
130 <option value="Pastel1_r">Pastel1 reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
131 <option value="Pastel2_r">Pastel2 reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
132 <option value="spring_r">spring reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
133 <option value="summer_r">summer reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
134 <option value="autumn_r">autumn reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
135 <option value="winter_r">winter reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
136 <option value="hot_r">hot reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
137 <option value="coolwarm_r">coolwarm reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
138 <option value="cool_r">cool reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
139 <option value="seismic_r">seismic reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
140 <option value="terrain_r">terrain reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
141 <option value="ocean_r">ocean reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
142 <option value="rainbow_r">rainbow reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
143 <option value="bone_r">bone reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
144 <option value="flag_r">flag reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
145 <option value="prism_r">prism reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
146 <option value="cubehelix_r">cubehelix reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
147 <option value="binary_r">binary reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
148 <option value="pink_r">pink reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
149 <option value="gray_r">gray reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
150 <option value="copper_r">copper reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
151 <option value="BrBG_r">BrBG reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
152 <option value="BuGn_r">BuGn reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
153 <option value="BuPu_r">BuPu reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
154 <option value="GnBu_r">GnBu reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
155 <option value="OrRd_r">OrRd reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
156 <option value="PiYG_r">PiYG reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
157 <option value="PRGn_r">PRGn reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
158 <option value="PuOr_r">PuOr reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
159 <option value="PuRd_r">PuRd reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
160 <option value="PuBu_r">PuBu reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
161 <option value="RdBu_r">RdBu reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
162 <option value="RdGy_r">RdGy reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
163 <option value="RdPu_r">RdPu reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
164 <option value="YlGn_r">YlGn reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
165 <option value="PuBuGn_r">PuBuGn reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
166 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
167 <option value="RdYlGn_r">RdYlGn reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
168 <option value="YlGnBu_r">YlGnBu reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
169 <option value="YlOrBr_r">YlOrBr reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
170 <option value="YlOrRd_r">YlOrRd reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
171 <option value="gist_gray_r">gist_gray reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
172 <option value="gist_stern_r">gist_stern reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
173 <option value="gist_earth_r">gist_earth reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
174 <option value="gist_yarg_r">gist_yarg reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
175 <option value="gist_ncar_r">gist_ncar reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
176 <option value="gist_rainbow_r">gist_rainbow reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
177 <option value="gist_heat_r">gist_heat reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
178 <option value="gnuplot_r">gnuplot reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
179 <option value="gnuplot2_r">gnuplot2 reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
180 <option value="CMRmap_r">CMRmap reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
181 <option value="bwr_r">bwr reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
182 <option value="hsv_r">hsv reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
183 <option value="brg_r">brg reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
184 <option value="jet_r">jet reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
185 <option value="afmhot_r">afmhot reversed</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
186 </param>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
187 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
188
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
189
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
190 <xml name="multiple_input_matrices">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
191 <repeat name="input_files" title="HiC Matrix files" min="2">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
192 <param name="matrix" type="data" format="h5,cool"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
193 label="HiC Matrix file"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
194 help=""/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
195 <param name="mlabel" type="text" size="30" optional="true" value=""
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
196 label="Label"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
197 help="Label to use in the output. If not given the dataset name will be used instead."/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
198 </repeat>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
199 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
200
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
201 <token name="@multiple_input_matrices@">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
202 #set $matrices = []
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
203 #set $mlabels = []
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
204 #for $counter, $i in enumerate($input_files):
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
205 ln -s $i.matrix #echo str($counter)+'_matrix'#;
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
206 #silent $matrices.append( '%s_matrix' % $counter )
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
207
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
208 #if str($i.mlabel.value) != "":
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
209 #set $mlabels += ['"%s"' % ($i.mlabel.value)]
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
210 #else
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
211 #set $mlabels += ['"%s"' % ($i.matrix.name)]
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
212 #end if
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
213 #end for
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
214 #set $mlabels = ' '.join($mlabels)
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
215 #set $matrices = ' '.join($matrices)
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
216 </token>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
217
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
218
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
219 <xml name="region">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
220 <param name="region" type="text" label="Region of the genome to limit the operation"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
221 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" argument="--region"/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
222 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
223
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
224
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
225
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
226 <xml name="kmeans_clustering">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
227 <conditional name="used_multiple_regions">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
228 <param name="used_multiple_regions_options" type="select"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
229 label="Did you compute the matrix with more than one groups of regions?"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
230 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.">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
231 <option value="yes">Yes, I used multiple groups of regions</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
232 <option value="no">No, I used only one group</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
233 </param>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
234 <when value="no">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
235 <conditional name="clustering">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
236 <param name="clustering_options" type="select" label="Clustering algorithm">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
237 <option value="none">No clustering</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
238 <option value="kmeans">Kmeans clustering</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
239 </param>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
240 <when value="kmeans">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
241 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
242 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)."/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
243 </when>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
244 <when value="none" />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
245 </conditional>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
246 </when>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
247 <when value="yes" />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
248 </conditional>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
249 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
250
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
251 <token name="@KMEANS_CLUSTERING@">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
252 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
253 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
254 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
255 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
256 #end if
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
257 #end if
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
258 #end if
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
259 </token>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
260
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
261 <xml name="samFlag">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
262 <param name="samFlag" type="integer" optional="true" value=""
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
263 label="Filter reads based on the SAM flag"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
264 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)"/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
265 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
266 <xml name="plotNumbers">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
267 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
268 label="Plot the correlation value"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
269 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
270 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
271 <xml name="doNotExtendPairedEnds">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
272 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
273 label="Do not extend paired ends"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
274 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)"/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
275 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
276
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
277 <xml name="ignoreDuplicates">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
278 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
279 label="Ignore duplicates"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
280 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)" />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
281 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
282
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
283 <xml name="minMappingQuality">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
284 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
285 label="Minimum mapping quality"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
286 help= "If set, only reads that have a mapping quality score higher than the given value are considered.
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
287 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
288 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."/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
289 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
290
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
291 <xml name="skipZeros">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
292 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
293 label ="Skip zeros"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
294 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)" />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
295 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
296
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
297 <xml name="fragmentLength">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
298 <param name="fragmentLength" type="integer" value="300" min="1"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
299 label="Fragment length used for the sequencing"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
300 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
301 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
302
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
303 <xml name="scaleFactor">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
304 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
305 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
306 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
307
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
308 <xml name="xMax">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
309 <param argument="--xMax" name="xMax" type="integer" optional="true" value=""
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
310 label="Max value for the x-axis in counts per bin" />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
311 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
312
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
313 <xml name="filterThreshold">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
314 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
315 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
316
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
317 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
318 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
319 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
320
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
321 <xml name="pseudocount">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
322 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
323 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
324 <xml name='matrix_h5_cooler_macro'>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
325 <param name='matrix_h5_cooler' type="data" format="h5,cool"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
326 label="Matrix to compute on"/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
327 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
328 <xml name='matrix_h5_cooler_multiple_macro'>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
329 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
330 label="Matricies to compute on" multiple="true"/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
331 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
332 <token name="@REFERENCES@">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
333
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
334 .. class:: infomark
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
335
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
336 For more information on the tools, please visit our `help site`_.
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
337
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
338 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
339
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
340 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
341
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
342 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
343 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
344 .. _help site: https://hicexplorer.readthedocs.org
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
345
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
346 </token>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
347
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
348
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
349 <xml name="multiple_input_bams">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
350 <repeat name="input_files" title="BAM files" min="2">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
351 <param name="bamfile" type="data" format="bam"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
352 label="Bam file"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
353 help="The BAM file must be sorted."/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
354 <param name="label" type="text" size="30" optional="true" value=""
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
355 label="Label"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
356 help="Label to use in the output. If not given the dataset name will be used instead."/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
357 </repeat>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
358 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
359
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
360 <xml name="multiple_input_bigwigs">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
361 <repeat name="input_files" title="BigWig files" min="2">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
362 <param name="bigwigfile" type="data" format="bigwig"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
363 label="Bigwig file"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
364 help="The Bigwig file must be sorted."/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
365 <param name="label" type="text" size="30" optional="true" value=""
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
366 label="Label"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
367 help="Label to use in the output. If not given the dataset name will be used instead."/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
368 </repeat>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
369 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
370
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
371 <xml name="plotTitle">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
372 <param name="plotTitle" type="text" value="" size="30" optional="True"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
373 label="Title of the plot"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
374 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
375 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
376
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
377 <token name="@multiple_input_bams@">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
378 #import tempfile
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
379 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
380 #set files=[]
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
381 #set labels=[]
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
382 #for $i in $input_files:
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
383 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
384 #set $temp_input_path = $temp_input_handle.name
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
385 #silent $temp_input_handle.close()
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
386 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
387 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
388 #silent $files.append('%s.bam' % $temp_input_path)
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
389
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
390 ##set $files += [str($i.bamfile)]
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
391 #if str($i.label.value) != "":
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
392 #set $labels += ["\"%s\"" % ($i.label.value)]
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
393 #else
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
394 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
395 #end if
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
396 #end for
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
397 </token>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
398
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
399 <token name="@multiple_input_bigwigs@">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
400 #import tempfile
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
401 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
402 #set files=[]
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
403 #set labels=[]
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
404 #for $i in $input_files:
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
405 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
406 #set $temp_input_path = $temp_input_handle.name
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
407 #silent $temp_input_handle.close()
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
408 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
409 #silent $files.append('%s.bw' % $temp_input_path)
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
410
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
411 ##set $files += [str($i.bigwigfile)]
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
412 #if str($i.label.value) != "":
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
413 #set $labels += ["\"%s\"" % ($i.label.value)]
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
414 #else
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
415 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
416 #end if
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
417 #end for
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
418 </token>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
419
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
420 <xml name="reference_genome_source">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
421 <conditional name="source">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
422 <param name="ref_source" type="select" label="Reference genome">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
423 <option value="cached">locally cached</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
424 <option value="history">in your history</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
425 </param>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
426 <when value="cached">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
427 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
428 <options from_data_table="deepTools_seqs">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
429 <filter type="sort_by" column="1" />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
430 <validator type="no_options" message="No indexes are available." />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
431 </options>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
432 </param>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
433 </when>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
434 <when value="history">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
435 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
436 </when>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
437 </conditional>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
438 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
439
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
440 <token name="@reference_genome_source@">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
441 #if $source.ref_source=="history":
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
442 --genome $source.input1
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
443 #else:
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
444 --genome "${source.input1_2bit.fields.path}"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
445 #end if
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
446 </token>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
447
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
448 <xml name="effectiveGenomeSize">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
449 <conditional name="effectiveGenomeSize">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
450 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
451 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.
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
452 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
453 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.">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
454 <option value="93260000">ce10 (93260000)</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
455 <option value="121400000">dm3 (121400000)</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
456 <option value="2451960000" selected="true">hg19 (2451960000)</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
457 <option value="2150570000">mm9 (2150570000)</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
458 <option value="specific">user specified</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
459 </param>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
460 <when value="specific">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
461 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
462 </when>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
463 <when value="2150570000" />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
464 <when value="2451960000" />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
465 <when value="121400000" />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
466 <when value="93260000" />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
467 </conditional>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
468 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
469
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
470 <xml name="image_file_format">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
471 <param name="outFileFormat" type="select" label="Image file format">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
472 <option value="png" selected="true">png</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
473 <option value="pdf">pdf</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
474 <option value="svg">svg</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
475 <option value="eps">eps</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
476 <option value="emf">emf</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
477 </param>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
478 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
479
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
480 <xml name="missingDataAsZero">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
481 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
482 label ="Treat missing data as zero"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
483 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." />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
484 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
485
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
486 <xml name="input_save_matrix_values">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
487 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
488 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
489
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
490 <xml name="input_graphic_output_settings">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
491 <conditional name="output" >
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
492 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
493 <option value="no" selected="true">no</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
494 <option value="yes">yes</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
495 </param>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
496 <when value="no" />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
497 <when value="yes">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
498 <yield />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
499 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
500 <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."/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
501 </when>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
502 </conditional>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
503 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
504
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
505 <xml name="input_image_file_format">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
506 <param name="outFileFormat" type="select" label="Image file format">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
507 <option value="png" selected="true">png</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
508 <option value="pdf">pdf</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
509 <option value="svg">svg</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
510 <option value="eps">eps</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
511 <option value="emf">emf</option>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
512 </param>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
513 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
514
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
515 <xml name="output_image_file_format">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
516 <data format="png" name="outFileName" label="${tool.name} image">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
517 <change_format>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
518 <when input="output.outFileFormat" value="pdf" format="pdf" />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
519 <when input="output.outFileFormat" value="svg" format="svg" />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
520 <when input="output.outFileFormat" value="eps" format="eps" />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
521 <when input="output.outFileFormat" value="emf" format="emf" />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
522 </change_format>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
523 </data>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
524 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
525
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
526 <xml name="output_save_matrix_values">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
527 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
528 <filter>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
529 ((
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
530 output['showOutputSettings'] == 'yes' and
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
531 output['saveMatrix'] is True
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
532 ))
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
533 </filter>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
534 </data>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
535 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
536
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
537 <xml name="output_graphic_outputs">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
538 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
539 <filter>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
540 ((
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
541 output['showOutputSettings'] == 'yes' and
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
542 output['saveData'] is True
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
543 ))
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
544 </filter>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
545 </data>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
546 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
547 <filter>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
548 ((
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
549 output['showOutputSettings'] == 'yes' and
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
550 output['saveSortedRegions'] is True
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
551 ))
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
552 </filter>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
553 </data>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
554 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
555
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
556 <xml name="track_input_h5_macro">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
557 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
558 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
559 <xml name="track_input_bed_macro">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
560 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
561 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
562 <xml name="track_input_bedgraph_macro">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
563 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
564 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
565 <xml name="track_input_bigwig_macro">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
566 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
567 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
568 <xml name="track_input_bedgraph_matrix_macro">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
569 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
570 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
571 <xml name="track_input_tabular_macro">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
572 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
573 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
574 <xml name="plot_title">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
575 <param name="title" type="text" optional="true" label="Plot title"/>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
576 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
577
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
578 <xml name="spacer_macro">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
579 <param name="spacer_width" type="float" value="" optional="True"
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
580 label="Include spacer at the end of the track." help="Width of the spacer." />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
581 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
582 <xml name="fontsize_macro">
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
583 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
584 </xml>
94fff1a6a899 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
585 </macros>