Mercurial > repos > bgruening > hicexplorer_hicmergematrixbins

annotate macros.xml @ 5:1111999ae668 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
author iuc
date Wed, 03 Jan 2018 13:19:56 -0500
parents 936741507eb1
children 0c6d98e9c6e8
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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>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
3
2a62d67cab68 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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3 <token name="@WRAPPER_VERSION@">2.0</token>
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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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4 <xml name="requirements">
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5 <requirements>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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6 <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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7 <yield />
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8 </requirements>
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9 <version_command>@BINARY@ --version</version_command>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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10 </xml>
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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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12 <xml name="citations">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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13 <citations>
4
936741507eb1 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 8def073a083b0619e366436a067a614555190058
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14 <citation type="doi">10.5281/zenodo.1133705</citation>
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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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15 <yield />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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16 </citations>
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17 </xml>
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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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19 <xml name="zMax">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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20 <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 -->
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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21 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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22
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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23 <xml name="colormap">
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24 <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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f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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25 <option value="RdYlBu">RdYlBu</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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26 <option value="Accent">Accent</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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27 <option value="Spectral">Spectral</option>
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28 <option value="Set1">Set1</option>
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29 <option value="Set2">Set2</option>
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30 <option value="Set3">Set3</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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31 <option value="Dark2">Dark2</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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32 <option value="Reds">Reds</option>
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33 <option value="Oranges">Oranges</option>
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34 <option value="Greens">Greens</option>
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35 <option value="Blues">Blues</option>
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36 <option value="Greys">Greys</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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37 <option value="Purples">Purples</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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38 <option value="Paired">Paired</option>
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39 <option value="Pastel1">Pastel1</option>
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40 <option value="Pastel2">Pastel2</option>
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41 <option value="spring">spring</option>
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42 <option value="summer">summer</option>
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43 <option value="autumn">autumn</option>
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44 <option value="winter">winter</option>
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45 <option value="hot">hot</option>
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46 <option value="coolwarm">coolwarm</option>
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47 <option value="cool">cool</option>
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48 <option value="seismic">seismic</option>
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49 <option value="terrain">terrain</option>
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50 <option value="ocean">ocean</option>
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51 <option value="rainbow">rainbow</option>
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52 <option value="bone">bone</option>
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53 <option value="flag">flag</option>
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54 <option value="prism">prism</option>
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55 <option value="cubehelix">cubehelix</option>
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56 <option value="binary">binary</option>
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57 <option value="pink">pink</option>
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58 <option value="gray">gray</option>
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59 <option value="copper">copper</option>
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60 <option value="BrBG">BrBG</option>
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61 <option value="BuGn">BuGn</option>
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62 <option value="BuPu">BuPu</option>
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63 <option value="GnBu">GnBu</option>
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64 <option value="OrRd">OrRd</option>
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65 <option value="PiYG">PiYG</option>
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66 <option value="PRGn">PRGn</option>
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67 <option value="PuOr">PuOr</option>
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68 <option value="PuRd">PuRd</option>
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69 <option value="PuBu">PuBu</option>
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70 <option value="RdBu">RdBu</option>
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71 <option value="RdGy">RdGy</option>
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72 <option value="RdPu">RdPu</option>
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73 <option value="YlGn">YlGn</option>
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74 <option value="PuBuGn">PuBuGn</option>
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75 <option value="RdYlGn">RdYlGn</option>
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76 <option value="YlGnBu">YlGnBu</option>
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77 <option value="YlOrBr">YlOrBr</option>
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78 <option value="YlOrRd">YlOrRd</option>
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79 <option value="gist_gray">gist_gray</option>
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80 <option value="gist_stern">gist_stern</option>
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81 <option value="gist_earth">gist_earth</option>
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82 <option value="gist_yarg">gist_yarg</option>
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83 <option value="gist_ncar">gist_ncar</option>
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84 <option value="gist_rainbow">gist_rainbow</option>
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85 <option value="gist_heat">gist_heat</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="gnuplot">gnuplot</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="gnuplot2">gnuplot2</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="CMRmap">CMRmap</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="bwr">bwr</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="hsv">hsv</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="brg">brg</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="jet">jet</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="afmhot">afmhot</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="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
95 <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
96 <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
97 <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
98 <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
99 <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
100 <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
101 <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
102 <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
103 <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
104 <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
105 <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
106 <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
107 <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
108 <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
109 <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
110 <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
111 <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
112 <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
113 <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
114 <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
115 <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
116 <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
117 <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
118 <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
119 <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
120 <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
121 <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
122 <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
123 <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
124 <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
125 <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
126 <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
127 <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
128 <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
129 <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
130 <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
131 <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
132 <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
133 <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
134 <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
135 <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
136 <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
137 <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
138 <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
139 <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
140 <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
141 <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
142 <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
143 <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
144 <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
145 <option value="YlGnBu_r">YlGnBu 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="YlOrBr_r">YlOrBr 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="YlOrRd_r">YlOrRd 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="gist_gray_r">gist_gray 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="gist_stern_r">gist_stern 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="gist_earth_r">gist_earth 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="gist_yarg_r">gist_yarg 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="gist_ncar_r">gist_ncar 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="gist_rainbow_r">gist_rainbow reversed</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
154 <option value="gist_heat_r">gist_heat 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="gnuplot_r">gnuplot 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="gnuplot2_r">gnuplot2 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="CMRmap_r">CMRmap 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="bwr_r">bwr 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="hsv_r">hsv 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="brg_r">brg 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="jet_r">jet reversed</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
162 <option value="afmhot_r">afmhot reversed</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
163 </param>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff changeset
164 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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165
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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166
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
167 <xml name="multiple_input_matrices">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff changeset
168 <repeat name="input_files" title="HiC Matrix files" min="2">
3
2a62d67cab68 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
iuc
parents: 2
diff changeset
169 <param name="matrix" type="data" format="h5,cool"
0
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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170 label="HiC Matrix file"
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171 help=""/>
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172 <param name="mlabel" type="text" size="30" optional="true" value=""
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173 label="Label"
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174 help="Label to use in the output. If not given the dataset name will be used instead."/>
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175 </repeat>
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176 </xml>
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177
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178 <token name="@multiple_input_matrices@">
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179 #set $matrices = []
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180 #set $mlabels = []
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181 #for $counter, $i in enumerate($input_files):
3
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182 ln -s $i.matrix #echo str($counter)+'_matrix'#;
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183 #silent $matrices.append( '%s_matrix' % $counter )
0
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184
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185 #if str($i.mlabel.value) != "":
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186 #set $mlabels += ['"%s"' % ($i.mlabel.value)]
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187 #else
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188 #set $mlabels += ['"%s"' % ($i.matrix.name)]
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189 #end if
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190 #end for
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191 #set $mlabels = ' '.join($mlabels)
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192 #set $matrices = ' '.join($matrices)
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193 </token>
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194
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195
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196 <xml name="region">
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197 <param name="region" type="text" label="Region of the genome to limit the operation"
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198 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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199 </xml>
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200
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201
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202
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203 <xml name="kmeans_clustering">
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204 <conditional name="used_multiple_regions">
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205 <param name="used_multiple_regions_options" type="select"
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206 label="Did you compute the matrix with more than one groups of regions?"
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207 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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208 <option value="yes">Yes, I used multiple groups of regions</option>
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209 <option value="no">No, I used only one group</option>
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210 </param>
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211 <when value="no">
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212 <conditional name="clustering">
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213 <param name="clustering_options" type="select" label="Clustering algorithm">
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214 <option value="none">No clustering</option>
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215 <option value="kmeans">Kmeans clustering</option>
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216 </param>
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217 <when value="kmeans">
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218 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
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219 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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220 </when>
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221 <when value="none" />
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222 </conditional>
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223 </when>
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224 <when value="yes" />
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225 </conditional>
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226 </xml>
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227
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228 <token name="@KMEANS_CLUSTERING@">
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229 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
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230 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
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231 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
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232 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
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233 #end if
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234 #end if
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235 #end if
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236 </token>
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237
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238 <xml name="samFlag">
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239 <param name="samFlag" type="integer" optional="true" value=""
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240 label="Filter reads based on the SAM flag"
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241 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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242 </xml>
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243 <xml name="plotNumbers">
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244 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
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245 label="Plot the correlation value"
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246 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
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247 </xml>
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248 <xml name="doNotExtendPairedEnds">
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249 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
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250 label="Do not extend paired ends"
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251 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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252 </xml>
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253
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254 <xml name="ignoreDuplicates">
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255 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
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256 label="Ignore duplicates"
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257 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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258 </xml>
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259
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260 <xml name="minMappingQuality">
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261 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1"
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262 label="Minimum mapping quality"
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263 help= "If set, only reads that have a mapping quality score higher than the given value are considered.
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264 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
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265 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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266 </xml>
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267
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268 <xml name="skipZeros">
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269 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
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270 label ="Skip zeros"
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271 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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272 </xml>
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273
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274 <xml name="fragmentLength">
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275 <param name="fragmentLength" type="integer" value="300" min="1"
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276 label="Fragment length used for the sequencing"
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277 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
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278 </xml>
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279
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280 <xml name="scaleFactor">
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281 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
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282 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
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283 </xml>
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284
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285 <xml name="xMax">
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286 <param argument="--xMax" name="xMax" type="integer" optional="true" value=""
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287 label="Max value for the x-axis in counts per bin" />
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288 </xml>
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289
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290 <xml name="filterThreshold">
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291 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"
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292 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/>
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293
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294 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"
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295 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>
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296 </xml>
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297
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298
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299 <xml name="pseudocount">
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300 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
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301 </xml>
3
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302 <xml name='matrix_h5_cooler_macro'>
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303 <param name='matrix_h5_cooler' type="data" format="h5,cool"
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304 label="Matrix to compute on."/>
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305
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306 </xml>
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307 <xml name='matrix_h5_cooler_multiple_macro'>
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308 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
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309 label="Matrix to compute on." multiple="True"/>
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310 </xml>
0
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311 <token name="@REFERENCES@">
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312
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313 .. class:: infomark
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314
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315 For more information on the tools, please visit our `help site`_.
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316
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317 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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318
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319 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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320
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321 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
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322 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
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323 .. _help site: https://hicexplorer.readthedocs.org
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324
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325 </token>
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326
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327
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328 <xml name="multiple_input_bams">
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329 <repeat name="input_files" title="BAM files" min="2">
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330 <param name="bamfile" type="data" format="bam"
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331 label="Bam file"
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332 help="The BAM file must be sorted."/>
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333 <param name="label" type="text" size="30" optional="true" value=""
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334 label="Label"
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335 help="Label to use in the output. If not given the dataset name will be used instead."/>
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336 </repeat>
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337 </xml>
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338
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339 <xml name="multiple_input_bigwigs">
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340 <repeat name="input_files" title="BigWig files" min="2">
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341 <param name="bigwigfile" type="data" format="bigwig"
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342 label="Bigwig file"
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343 help="The Bigwig file must be sorted."/>
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344 <param name="label" type="text" size="30" optional="true" value=""
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345 label="Label"
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346 help="Label to use in the output. If not given the dataset name will be used instead."/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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347 </repeat>
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348 </xml>
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349
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350 <xml name="plotTitle">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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351 <param name="plotTitle" type="text" value="" size="30" optional="True"
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352 label="Title of the plot"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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353 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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354 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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355
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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356 <token name="@multiple_input_bams@">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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357 #import tempfile
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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358 #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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359 #set files=[]
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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360 #set labels=[]
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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361 #for $i in $input_files:
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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362 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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363 #set $temp_input_path = $temp_input_handle.name
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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364 #silent $temp_input_handle.close()
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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365 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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366 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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367 #silent $files.append('%s.bam' % $temp_input_path)
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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368
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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369 ##set $files += [str($i.bamfile)]
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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370 #if str($i.label.value) != "":
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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371 #set $labels += ["\"%s\"" % ($i.label.value)]
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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372 #else
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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373 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
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374 #end if
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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375 #end for
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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376 </token>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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377
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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378 <token name="@multiple_input_bigwigs@">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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379 #import tempfile
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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380 #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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381 #set files=[]
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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382 #set labels=[]
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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383 #for $i in $input_files:
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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384 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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385 #set $temp_input_path = $temp_input_handle.name
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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386 #silent $temp_input_handle.close()
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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387 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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388 #silent $files.append('%s.bw' % $temp_input_path)
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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389
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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390 ##set $files += [str($i.bigwigfile)]
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391 #if str($i.label.value) != "":
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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392 #set $labels += ["\"%s\"" % ($i.label.value)]
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393 #else
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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394 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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395 #end if
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396 #end for
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397 </token>
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398
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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399 <xml name="reference_genome_source">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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400 <conditional name="source">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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401 <param name="ref_source" type="select" label="Reference genome">
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402 <option value="cached">locally cached</option>
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403 <option value="history">in your history</option>
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404 </param>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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405 <when value="cached">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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406 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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407 <options from_data_table="deepTools_seqs">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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408 <filter type="sort_by" column="1" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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409 <validator type="no_options" message="No indexes are available." />
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410 </options>
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411 </param>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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412 </when>
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413 <when value="history">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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414 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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415 </when>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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416 </conditional>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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417 </xml>
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418
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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419 <token name="@reference_genome_source@">
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420 #if $source.ref_source=="history":
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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421 --genome $source.input1
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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422 #else:
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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423 --genome "${source.input1_2bit.fields.path}"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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424 #end if
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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425 </token>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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426
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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427 <xml name="effectiveGenomeSize">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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428 <conditional name="effectiveGenomeSize">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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429 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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430 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.
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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431 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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432 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.">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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433 <option value="93260000">ce10 (93260000)</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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434 <option value="121400000">dm3 (121400000)</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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435 <option value="2451960000" selected="true">hg19 (2451960000)</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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436 <option value="2150570000">mm9 (2150570000)</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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437 <option value="specific">user specified</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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438 </param>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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439 <when value="specific">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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440 <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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441 </when>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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442 <when value="2150570000" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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443 <when value="2451960000" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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444 <when value="121400000" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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445 <when value="93260000" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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446 </conditional>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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447 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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448
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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449 <xml name="image_file_format">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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450 <param name="outFileFormat" type="select" label="Image file format">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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451 <option value="png" selected="true">png</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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452 <option value="pdf">pdf</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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453 <option value="svg">svg</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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454 <option value="eps">eps</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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455 <option value="emf">emf</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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456 </param>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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457 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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458
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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459 <xml name="missingDataAsZero">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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460 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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461 label ="Treat missing data as zero"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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462 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." />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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463 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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464
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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465 <xml name="input_save_matrix_values">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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466 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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467 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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468
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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469 <xml name="input_graphic_output_settings">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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470 <conditional name="output" >
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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471 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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472 <option value="no" selected="true">no</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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473 <option value="yes">yes</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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474 </param>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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475 <when value="no" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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476 <when value="yes">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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477 <yield />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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478 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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479 <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."/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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480 </when>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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481 </conditional>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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482 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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483
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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484 <xml name="input_image_file_format">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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485 <param name="outFileFormat" type="select" label="Image file format">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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486 <option value="png" selected="true">png</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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487 <option value="pdf">pdf</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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488 <option value="svg">svg</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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489 <option value="eps">eps</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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490 <option value="emf">emf</option>
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491 </param>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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492 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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493
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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494 <xml name="output_image_file_format">
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495 <data format="png" name="outFileName" label="${tool.name} image">
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496 <change_format>
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497 <when input="output.outFileFormat" value="pdf" format="pdf" />
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498 <when input="output.outFileFormat" value="svg" format="svg" />
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499 <when input="output.outFileFormat" value="eps" format="eps" />
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500 <when input="output.outFileFormat" value="emf" format="emf" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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501 </change_format>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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502 </data>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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503 </xml>
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504
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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505 <xml name="output_save_matrix_values">
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506 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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507 <filter>
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508 ((
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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509 output['showOutputSettings'] == 'yes' and
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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510 output['saveMatrix'] is True
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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511 ))
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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512 </filter>
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513 </data>
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514 </xml>
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515
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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516 <xml name="output_graphic_outputs">
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517 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
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518 <filter>
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519 ((
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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520 output['showOutputSettings'] == 'yes' and
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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521 output['saveData'] is True
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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522 ))
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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523 </filter>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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524 </data>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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525 <data format="bed" name="outFileSortedRegions" label="${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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526 <filter>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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527 ((
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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528 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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529 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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530 ))
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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531 </filter>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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532 </data>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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533 </xml>
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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535 <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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536 <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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537 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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538 <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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539 <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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540 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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541 <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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542 <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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543 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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544 <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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545 <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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546 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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547 <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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548 <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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549 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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550 <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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551 <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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552 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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553 <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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554 <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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555 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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556
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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557 <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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558 <param name="spacer_width" type="float" value="" optional="True"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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559 label="Include spacer at the end of the track." help="Width of the spacer." />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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560 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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561 <xml name="fontsize_macro">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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562 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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563 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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564 </macros>