Mercurial > repos > bgruening > hicexplorer_hicmergematrixbins

annotate macros.xml @ 6:0c6d98e9c6e8 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
author iuc
date Wed, 07 Mar 2018 02:25:20 -0500 (2018-03-07)
parents 936741507eb1
children d444ca8616f5
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f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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1 <macros>
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2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
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0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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3 <token name="@WRAPPER_VERSION@">2.1</token>
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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5 <token name="@USE_RANGE@">
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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6 #if $use_range.select_use_range == "yes_use_range":
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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7 --range $range_min:$range_max
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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8 #end if
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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9 </token>
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10
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11 <xml name="requirements">
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12 <requirements>
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13 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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14 <yield />
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15 </requirements>
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16 <version_command>@BINARY@ --version</version_command>
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17 </xml>
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19 <xml name="citations">
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20 <citations>
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21 <citation type="doi">10.5281/zenodo.1133705</citation>
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22 <yield />
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23 </citations>
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24 </xml>
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26 <xml name="zMax">
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27 <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 -->
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28 </xml>
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29 <xml name="use_range">
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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30 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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31 <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range">
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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32 <option value="no_use_range">No restriction</option>
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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33 <option value="yes_use_range">Only consider counts within a range</option>
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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34 </param>
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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35 <when value="no_use_range"/>
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36 <when value="yes_use_range">
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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37 <expand macro='range' />
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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38 </when>
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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39 </conditional>
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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40 </xml>
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41
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42 <xml name="range">
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43 <param name="range_min" type="integer" value="" min="0"/>
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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44 <param name="range_max" type="integer" value="" min="0"/>
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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45 </xml>
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46
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47 <xml name="colormap">
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48 <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
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49 <option value="RdYlBu">RdYlBu</option>
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50 <option value="Accent">Accent</option>
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51 <option value="Spectral">Spectral</option>
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52 <option value="Set1">Set1</option>
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53 <option value="Set2">Set2</option>
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54 <option value="Set3">Set3</option>
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55 <option value="Dark2">Dark2</option>
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56 <option value="Reds">Reds</option>
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57 <option value="Oranges">Oranges</option>
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58 <option value="Greens">Greens</option>
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59 <option value="Blues">Blues</option>
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60 <option value="Greys">Greys</option>
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61 <option value="Purples">Purples</option>
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62 <option value="Paired">Paired</option>
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63 <option value="Pastel1">Pastel1</option>
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64 <option value="Pastel2">Pastel2</option>
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65 <option value="spring">spring</option>
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66 <option value="summer">summer</option>
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67 <option value="autumn">autumn</option>
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68 <option value="winter">winter</option>
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69 <option value="hot">hot</option>
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70 <option value="coolwarm">coolwarm</option>
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71 <option value="cool">cool</option>
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72 <option value="seismic">seismic</option>
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73 <option value="terrain">terrain</option>
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74 <option value="ocean">ocean</option>
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75 <option value="rainbow">rainbow</option>
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76 <option value="bone">bone</option>
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77 <option value="flag">flag</option>
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78 <option value="prism">prism</option>
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79 <option value="cubehelix">cubehelix</option>
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80 <option value="binary">binary</option>
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81 <option value="pink">pink</option>
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82 <option value="gray">gray</option>
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83 <option value="copper">copper</option>
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84 <option value="BrBG">BrBG</option>
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85 <option value="BuGn">BuGn</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
86 <option value="BuPu">BuPu</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
87 <option value="GnBu">GnBu</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
88 <option value="OrRd">OrRd</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
89 <option value="PiYG">PiYG</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
90 <option value="PRGn">PRGn</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
91 <option value="PuOr">PuOr</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
92 <option value="PuRd">PuRd</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
93 <option value="PuBu">PuBu</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
94 <option value="RdBu">RdBu</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
95 <option value="RdGy">RdGy</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
96 <option value="RdPu">RdPu</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
97 <option value="YlGn">YlGn</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
98 <option value="PuBuGn">PuBuGn</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
99 <option value="RdYlGn">RdYlGn</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
100 <option value="YlGnBu">YlGnBu</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
101 <option value="YlOrBr">YlOrBr</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
102 <option value="YlOrRd">YlOrRd</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff changeset
103 <option value="gist_gray">gist_gray</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff changeset
104 <option value="gist_stern">gist_stern</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
105 <option value="gist_earth">gist_earth</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff changeset
106 <option value="gist_yarg">gist_yarg</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
107 <option value="gist_ncar">gist_ncar</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
108 <option value="gist_rainbow">gist_rainbow</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
109 <option value="gist_heat">gist_heat</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff changeset
110 <option value="gnuplot">gnuplot</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
111 <option value="gnuplot2">gnuplot2</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff changeset
112 <option value="CMRmap">CMRmap</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff changeset
113 <option value="bwr">bwr</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff changeset
114 <option value="hsv">hsv</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff changeset
115 <option value="brg">brg</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff changeset
116 <option value="jet">jet</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
117 <option value="afmhot">afmhot</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff changeset
118 <option value="Accent_r">Accent reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
119 <option value="Spectral_r">Spectral reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
120 <option value="Set1_r">Set1 reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
121 <option value="Set2_r">Set2 reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
122 <option value="Set3_r">Set3 reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
123 <option value="Dark2_r">Dark2 reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
124 <option value="Reds_r">Reds reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
125 <option value="Oranges_r">Oranges reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
126 <option value="Greens_r">Greens reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
127 <option value="Blues_r">Blues reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
128 <option value="Greys_r">Greys reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
129 <option value="Purples_r">Purples reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
130 <option value="Paired_r">Paired reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
131 <option value="Pastel1_r">Pastel1 reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
132 <option value="Pastel2_r">Pastel2 reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
133 <option value="spring_r">spring reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
134 <option value="summer_r">summer reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
135 <option value="autumn_r">autumn reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
136 <option value="winter_r">winter reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
137 <option value="hot_r">hot reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
138 <option value="coolwarm_r">coolwarm reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
139 <option value="cool_r">cool reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
140 <option value="seismic_r">seismic reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
141 <option value="terrain_r">terrain reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
142 <option value="ocean_r">ocean reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
143 <option value="rainbow_r">rainbow reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
144 <option value="bone_r">bone reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
145 <option value="flag_r">flag reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
146 <option value="prism_r">prism reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
147 <option value="cubehelix_r">cubehelix reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
148 <option value="binary_r">binary reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
149 <option value="pink_r">pink reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
150 <option value="gray_r">gray reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
151 <option value="copper_r">copper reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
152 <option value="BrBG_r">BrBG reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
153 <option value="BuGn_r">BuGn reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
154 <option value="BuPu_r">BuPu reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
155 <option value="GnBu_r">GnBu reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
156 <option value="OrRd_r">OrRd reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
157 <option value="PiYG_r">PiYG reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
158 <option value="PRGn_r">PRGn reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
159 <option value="PuOr_r">PuOr reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
160 <option value="PuRd_r">PuRd reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
161 <option value="PuBu_r">PuBu reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
162 <option value="RdBu_r">RdBu reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
163 <option value="RdGy_r">RdGy reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
164 <option value="RdPu_r">RdPu reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
165 <option value="YlGn_r">YlGn reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
166 <option value="PuBuGn_r">PuBuGn reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
167 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
168 <option value="RdYlGn_r">RdYlGn reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
169 <option value="YlGnBu_r">YlGnBu reversed</option>
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170 <option value="YlOrBr_r">YlOrBr reversed</option>
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171 <option value="YlOrRd_r">YlOrRd reversed</option>
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172 <option value="gist_gray_r">gist_gray reversed</option>
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173 <option value="gist_stern_r">gist_stern reversed</option>
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174 <option value="gist_earth_r">gist_earth reversed</option>
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175 <option value="gist_yarg_r">gist_yarg reversed</option>
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176 <option value="gist_ncar_r">gist_ncar reversed</option>
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177 <option value="gist_rainbow_r">gist_rainbow reversed</option>
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178 <option value="gist_heat_r">gist_heat reversed</option>
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179 <option value="gnuplot_r">gnuplot reversed</option>
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180 <option value="gnuplot2_r">gnuplot2 reversed</option>
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181 <option value="CMRmap_r">CMRmap reversed</option>
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182 <option value="bwr_r">bwr reversed</option>
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183 <option value="hsv_r">hsv reversed</option>
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184 <option value="brg_r">brg reversed</option>
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185 <option value="jet_r">jet reversed</option>
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186 <option value="afmhot_r">afmhot reversed</option>
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187 </param>
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188 </xml>
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189
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190
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191 <xml name="multiple_input_matrices">
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192 <repeat name="input_files" title="HiC Matrix files" min="2">
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193 <param name="matrix" type="data" format="h5,cool"
0
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194 label="HiC Matrix file"
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195 help=""/>
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196 <param name="mlabel" type="text" size="30" optional="true" value=""
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197 label="Label"
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198 help="Label to use in the output. If not given the dataset name will be used instead."/>
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199 </repeat>
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200 </xml>
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201
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202 <token name="@multiple_input_matrices@">
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203 #set $matrices = []
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204 #set $mlabels = []
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205 #for $counter, $i in enumerate($input_files):
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206 ln -s $i.matrix #echo str($counter)+'_matrix'#;
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207 #silent $matrices.append( '%s_matrix' % $counter )
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208
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209 #if str($i.mlabel.value) != "":
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210 #set $mlabels += ['"%s"' % ($i.mlabel.value)]
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211 #else
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212 #set $mlabels += ['"%s"' % ($i.matrix.name)]
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213 #end if
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214 #end for
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215 #set $mlabels = ' '.join($mlabels)
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216 #set $matrices = ' '.join($matrices)
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217 </token>
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218
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219
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220 <xml name="region">
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221 <param name="region" type="text" label="Region of the genome to limit the operation"
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222 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" argument="--region"/>
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223 </xml>
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224
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225
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226
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227 <xml name="kmeans_clustering">
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228 <conditional name="used_multiple_regions">
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229 <param name="used_multiple_regions_options" type="select"
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230 label="Did you compute the matrix with more than one groups of regions?"
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231 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
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232 <option value="yes">Yes, I used multiple groups of regions</option>
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233 <option value="no">No, I used only one group</option>
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234 </param>
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235 <when value="no">
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236 <conditional name="clustering">
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237 <param name="clustering_options" type="select" label="Clustering algorithm">
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238 <option value="none">No clustering</option>
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239 <option value="kmeans">Kmeans clustering</option>
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240 </param>
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241 <when value="kmeans">
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242 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
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243 help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/>
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244 </when>
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245 <when value="none" />
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246 </conditional>
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247 </when>
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248 <when value="yes" />
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249 </conditional>
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250 </xml>
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251
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252 <token name="@KMEANS_CLUSTERING@">
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253 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
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254 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
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255 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
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256 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
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257 #end if
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258 #end if
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259 #end if
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260 </token>
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261
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262 <xml name="samFlag">
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263 <param name="samFlag" type="integer" optional="true" value=""
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264 label="Filter reads based on the SAM flag"
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265 help= "For example to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage. (--samFlag)"/>
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266 </xml>
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267 <xml name="plotNumbers">
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268 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
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269 label="Plot the correlation value"
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270 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
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271 </xml>
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272 <xml name="doNotExtendPairedEnds">
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273 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
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274 label="Do not extend paired ends"
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275 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available. (--doNotExtendPairedEnds)"/>
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276 </xml>
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277
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278 <xml name="ignoreDuplicates">
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279 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
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280 label="Ignore duplicates"
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281 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read. (--ignoreDuplicates)" />
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282 </xml>
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283
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284 <xml name="minMappingQuality">
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285 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1"
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286 label="Minimum mapping quality"
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287 help= "If set, only reads that have a mapping quality score higher than the given value are considered.
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288 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
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289 A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
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290 </xml>
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291
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292 <xml name="skipZeros">
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293 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
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294 label ="Skip zeros"
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295 help ="If set, then zero counts that happen for *all* BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined. (--skipZeros)" />
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296 </xml>
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297
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298 <xml name="fragmentLength">
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299 <param name="fragmentLength" type="integer" value="300" min="1"
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300 label="Fragment length used for the sequencing"
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301 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
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302 </xml>
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303
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304 <xml name="scaleFactor">
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305 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
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306 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
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307 </xml>
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308
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309 <xml name="xMax">
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310 <param argument="--xMax" name="xMax" type="integer" optional="true" value=""
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311 label="Max value for the x-axis in counts per bin" />
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312 </xml>
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313
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314 <xml name="filterThreshold">
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315 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"
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316 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/>
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317
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318 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"
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319 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>
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320 </xml>
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321
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322
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323 <xml name="pseudocount">
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324 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
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325 </xml>
3
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326 <xml name='matrix_h5_cooler_macro'>
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327 <param name='matrix_h5_cooler' type="data" format="h5,cool"
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328 label="Matrix to compute on"/>
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329 </xml>
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330 <xml name='matrix_h5_cooler_multiple_macro'>
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331 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
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332 label="Matricies to compute on" multiple="true"/>
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333 </xml>
0
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334 <token name="@REFERENCES@">
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335
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336 .. class:: infomark
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337
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338 For more information on the tools, please visit our `help site`_.
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339
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340 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
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341
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342 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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343
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344 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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345 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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346 .. _help site: https://hicexplorer.readthedocs.org
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347
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348 </token>
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349
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350
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351 <xml name="multiple_input_bams">
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352 <repeat name="input_files" title="BAM files" min="2">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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353 <param name="bamfile" type="data" format="bam"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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354 label="Bam file"
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355 help="The BAM file must be sorted."/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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356 <param name="label" type="text" size="30" optional="true" value=""
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357 label="Label"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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358 help="Label to use in the output. If not given the dataset name will be used instead."/>
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359 </repeat>
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360 </xml>
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361
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362 <xml name="multiple_input_bigwigs">
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363 <repeat name="input_files" title="BigWig files" min="2">
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364 <param name="bigwigfile" type="data" format="bigwig"
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365 label="Bigwig file"
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366 help="The Bigwig file must be sorted."/>
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367 <param name="label" type="text" size="30" optional="true" value=""
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368 label="Label"
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369 help="Label to use in the output. If not given the dataset name will be used instead."/>
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370 </repeat>
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371 </xml>
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372
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373 <xml name="plotTitle">
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374 <param name="plotTitle" type="text" value="" size="30" optional="True"
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375 label="Title of the plot"
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376 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
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377 </xml>
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378
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379 <token name="@multiple_input_bams@">
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380 #import tempfile
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381 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
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382 #set files=[]
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383 #set labels=[]
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384 #for $i in $input_files:
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385 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
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386 #set $temp_input_path = $temp_input_handle.name
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387 #silent $temp_input_handle.close()
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388 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
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389 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
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390 #silent $files.append('%s.bam' % $temp_input_path)
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391
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392 ##set $files += [str($i.bamfile)]
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393 #if str($i.label.value) != "":
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394 #set $labels += ["\"%s\"" % ($i.label.value)]
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395 #else
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396 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
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397 #end if
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398 #end for
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399 </token>
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400
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401 <token name="@multiple_input_bigwigs@">
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402 #import tempfile
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403 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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404 #set files=[]
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405 #set labels=[]
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406 #for $i in $input_files:
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407 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
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408 #set $temp_input_path = $temp_input_handle.name
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409 #silent $temp_input_handle.close()
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410 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
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411 #silent $files.append('%s.bw' % $temp_input_path)
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412
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413 ##set $files += [str($i.bigwigfile)]
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414 #if str($i.label.value) != "":
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415 #set $labels += ["\"%s\"" % ($i.label.value)]
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416 #else
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417 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
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418 #end if
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419 #end for
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420 </token>
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421
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422 <xml name="reference_genome_source">
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423 <conditional name="source">
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424 <param name="ref_source" type="select" label="Reference genome">
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425 <option value="cached">locally cached</option>
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426 <option value="history">in your history</option>
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427 </param>
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428 <when value="cached">
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429 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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430 <options from_data_table="deepTools_seqs">
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431 <filter type="sort_by" column="1" />
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432 <validator type="no_options" message="No indexes are available." />
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433 </options>
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434 </param>
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435 </when>
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436 <when value="history">
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437 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
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438 </when>
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439 </conditional>
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440 </xml>
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441
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442 <token name="@reference_genome_source@">
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443 #if $source.ref_source=="history":
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444 --genome $source.input1
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445 #else:
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446 --genome "${source.input1_2bit.fields.path}"
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447 #end if
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448 </token>
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449
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450 <xml name="effectiveGenomeSize">
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451 <conditional name="effectiveGenomeSize">
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452 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
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453 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
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454 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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455 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
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456 <option value="93260000">ce10 (93260000)</option>
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457 <option value="121400000">dm3 (121400000)</option>
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458 <option value="2451960000" selected="true">hg19 (2451960000)</option>
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459 <option value="2150570000">mm9 (2150570000)</option>
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460 <option value="specific">user specified</option>
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461 </param>
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462 <when value="specific">
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463 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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464 </when>
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465 <when value="2150570000" />
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466 <when value="2451960000" />
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467 <when value="121400000" />
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468 <when value="93260000" />
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469 </conditional>
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470 </xml>
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471
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472 <xml name="image_file_format">
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473 <param name="outFileFormat" type="select" label="Image file format">
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474 <option value="png" selected="true">png</option>
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475 <option value="pdf">pdf</option>
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476 <option value="svg">svg</option>
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477 <option value="eps">eps</option>
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478 <option value="emf">emf</option>
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479 </param>
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480 </xml>
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481
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482 <xml name="missingDataAsZero">
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483 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
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484 label ="Treat missing data as zero"
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485 help ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />
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486 </xml>
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487
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488 <xml name="input_save_matrix_values">
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489 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
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490 </xml>
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491
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492 <xml name="input_graphic_output_settings">
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493 <conditional name="output" >
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494 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
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495 <option value="no" selected="true">no</option>
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496 <option value="yes">yes</option>
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497 </param>
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498 <when value="no" />
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499 <when value="yes">
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500 <yield />
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501 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
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502 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
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503 </when>
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504 </conditional>
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505 </xml>
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506
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507 <xml name="input_image_file_format">
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508 <param name="outFileFormat" type="select" label="Image file format">
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509 <option value="png" selected="true">png</option>
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510 <option value="pdf">pdf</option>
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511 <option value="svg">svg</option>
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512 <option value="eps">eps</option>
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513 <option value="emf">emf</option>
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514 </param>
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515 </xml>
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516
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517 <xml name="output_image_file_format">
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518 <data format="png" name="outFileName" label="${tool.name} image">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
519 <change_format>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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520 <when input="output.outFileFormat" value="pdf" format="pdf" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
521 <when input="output.outFileFormat" value="svg" format="svg" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
522 <when input="output.outFileFormat" value="eps" format="eps" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
523 <when input="output.outFileFormat" value="emf" format="emf" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
524 </change_format>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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525 </data>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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526 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
527
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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528 <xml name="output_save_matrix_values">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
529 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
530 <filter>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
531 ((
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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532 output['showOutputSettings'] == 'yes' and
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
533 output['saveMatrix'] is True
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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534 ))
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
535 </filter>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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536 </data>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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537 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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538
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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539 <xml name="output_graphic_outputs">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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540 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff changeset
541 <filter>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
542 ((
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
543 output['showOutputSettings'] == 'yes' and
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
544 output['saveData'] is True
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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545 ))
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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546 </filter>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
547 </data>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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548 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
549 <filter>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
550 ((
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff changeset
551 output['showOutputSettings'] == 'yes' and
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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552 output['saveSortedRegions'] is True
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
553 ))
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
554 </filter>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
555 </data>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
556 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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557
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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558 <xml name="track_input_h5_macro">
3
2a62d67cab68 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
559 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>
0
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
560 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
561 <xml name="track_input_bed_macro">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
562 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
563 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
564 <xml name="track_input_bedgraph_macro">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
565 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
566 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
567 <xml name="track_input_bigwig_macro">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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568 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
569 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
570 <xml name="track_input_bedgraph_matrix_macro">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
571 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
572 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
573 <xml name="track_input_tabular_macro">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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574 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
575 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
576 <xml name="plot_title">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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577 <param name="title" type="text" optional="true" label="Plot title"/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
578 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
579
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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580 <xml name="spacer_macro">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
581 <param name="spacer_width" type="float" value="" optional="True"
6
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents: 4
diff changeset
582 label="Include spacer at the end of the track." help="Width of the spacer." />
0
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
583 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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584 <xml name="fontsize_macro">
6
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents: 4
diff changeset
585 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
0
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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586 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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587 </macros>