Mercurial > repos > bgruening > hicexplorer_hiccorrelate

annotate macros.xml @ 2:31dbc867e271 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
author bgruening
date Mon, 03 Apr 2017 06:19:32 -0400
parents 3fc885f53423
children 4ef71736c95a
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1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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1 <macros>
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2 <xml name="stdio">
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3 <stdio>
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4 <exit_code range="1:" />
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5 <exit_code range=":-1" />
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6 <regex match="Error:" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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7 <regex match="Exception:" />
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8 <regex match="EXception:" />
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9 <regex match="Traceback" />
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10 </stdio>
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11 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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12
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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13 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
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31dbc867e271 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
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14 <token name="@WRAPPER_VERSION@">1.7.2</token>
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15 <xml name="requirements">
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16 <requirements>
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17 <requirement type="package" version="2.7.13">python</requirement>
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18 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
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19 <yield />
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20 </requirements>
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21 <expand macro="stdio" />
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22 <version_command>@BINARY@ --version</version_command>
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23 </xml>
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25 <xml name="citations">
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26 <citations>
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27 <citation type="doi">10.5281/zenodo.159780</citation>
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28 <yield />
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29 </citations>
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30 </xml>
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31
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32 <xml name="zMax">
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33 <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow -->
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34 </xml>
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35
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36 <xml name="colormap">
1
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37 <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: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
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38 <option value="RdYlBu">RdYlBu</option>
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39 <option value="Accent">Accent</option>
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40 <option value="Spectral">Spectral</option>
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41 <option value="Set1">Set1</option>
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42 <option value="Set2">Set2</option>
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43 <option value="Set3">Set3</option>
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44 <option value="Dark2">Dark2</option>
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45 <option value="Reds">Reds</option>
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46 <option value="Oranges">Oranges</option>
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47 <option value="Greens">Greens</option>
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48 <option value="Blues">Blues</option>
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49 <option value="Greys">Greys</option>
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50 <option value="Purples">Purples</option>
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51 <option value="Paired">Paired</option>
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52 <option value="Pastel1">Pastel1</option>
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53 <option value="Pastel2">Pastel2</option>
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54 <option value="spring">spring</option>
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55 <option value="summer">summer</option>
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56 <option value="autumn">autumn</option>
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57 <option value="winter">winter</option>
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58 <option value="hot">hot</option>
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59 <option value="coolwarm">coolwarm</option>
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60 <option value="cool">cool</option>
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61 <option value="seismic">seismic</option>
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62 <option value="terrain">terrain</option>
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63 <option value="ocean">ocean</option>
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64 <option value="rainbow">rainbow</option>
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65 <option value="bone">bone</option>
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66 <option value="flag">flag</option>
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67 <option value="prism">prism</option>
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68 <option value="cubehelix">cubehelix</option>
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69 <option value="binary">binary</option>
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70 <option value="pink">pink</option>
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71 <option value="gray">gray</option>
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72 <option value="copper">copper</option>
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73 <option value="BrBG">BrBG</option>
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74 <option value="BuGn">BuGn</option>
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75 <option value="BuPu">BuPu</option>
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76 <option value="GnBu">GnBu</option>
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77 <option value="OrRd">OrRd</option>
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78 <option value="PiYG">PiYG</option>
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79 <option value="PRGn">PRGn</option>
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80 <option value="PuOr">PuOr</option>
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81 <option value="PuRd">PuRd</option>
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82 <option value="PuBu">PuBu</option>
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83 <option value="RdBu">RdBu</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
84 <option value="RdGy">RdGy</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
85 <option value="RdPu">RdPu</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
86 <option value="YlGn">YlGn</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
87 <option value="PuBuGn">PuBuGn</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
88 <option value="RdYlGn">RdYlGn</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
89 <option value="YlGnBu">YlGnBu</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
90 <option value="YlOrBr">YlOrBr</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
91 <option value="YlOrRd">YlOrRd</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
92 <option value="gist_gray">gist_gray</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
93 <option value="gist_stern">gist_stern</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
94 <option value="gist_earth">gist_earth</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
95 <option value="gist_yarg">gist_yarg</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
96 <option value="gist_ncar">gist_ncar</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
97 <option value="gist_rainbow">gist_rainbow</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
98 <option value="gist_heat">gist_heat</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
99 <option value="gnuplot">gnuplot</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
100 <option value="gnuplot2">gnuplot2</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
101 <option value="CMRmap">CMRmap</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
102 <option value="bwr">bwr</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
103 <option value="hsv">hsv</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
104 <option value="brg">brg</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
105 <option value="jet">jet</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
106 <option value="afmhot">afmhot</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
107 <option value="Accent_r">Accent reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
108 <option value="Spectral_r">Spectral reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
109 <option value="Set1_r">Set1 reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
110 <option value="Set2_r">Set2 reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
111 <option value="Set3_r">Set3 reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
112 <option value="Dark2_r">Dark2 reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
113 <option value="Reds_r">Reds reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
114 <option value="Oranges_r">Oranges reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
115 <option value="Greens_r">Greens reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
116 <option value="Blues_r">Blues reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
117 <option value="Greys_r">Greys reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
118 <option value="Purples_r">Purples reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
119 <option value="Paired_r">Paired reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
120 <option value="Pastel1_r">Pastel1 reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
121 <option value="Pastel2_r">Pastel2 reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
122 <option value="spring_r">spring reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
123 <option value="summer_r">summer reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
124 <option value="autumn_r">autumn reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
125 <option value="winter_r">winter reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
126 <option value="hot_r">hot reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
127 <option value="coolwarm_r">coolwarm reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
128 <option value="cool_r">cool reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
129 <option value="seismic_r">seismic reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
130 <option value="terrain_r">terrain reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
131 <option value="ocean_r">ocean reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
132 <option value="rainbow_r">rainbow reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
133 <option value="bone_r">bone reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
134 <option value="flag_r">flag reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
135 <option value="prism_r">prism reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
136 <option value="cubehelix_r">cubehelix reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
137 <option value="binary_r">binary reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
138 <option value="pink_r">pink reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
139 <option value="gray_r">gray reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
140 <option value="copper_r">copper reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
141 <option value="BrBG_r">BrBG reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
142 <option value="BuGn_r">BuGn reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
143 <option value="BuPu_r">BuPu reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
144 <option value="GnBu_r">GnBu reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
145 <option value="OrRd_r">OrRd reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
146 <option value="PiYG_r">PiYG reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
147 <option value="PRGn_r">PRGn reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
148 <option value="PuOr_r">PuOr reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
149 <option value="PuRd_r">PuRd reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
150 <option value="PuBu_r">PuBu reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
151 <option value="RdBu_r">RdBu reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
152 <option value="RdGy_r">RdGy reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
153 <option value="RdPu_r">RdPu reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
154 <option value="YlGn_r">YlGn reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
155 <option value="PuBuGn_r">PuBuGn reversed</option>
1
3fc885f53423 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents: 0
diff changeset
156 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
0
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
157 <option value="RdYlGn_r">RdYlGn reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
158 <option value="YlGnBu_r">YlGnBu reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
159 <option value="YlOrBr_r">YlOrBr reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
160 <option value="YlOrRd_r">YlOrRd reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
161 <option value="gist_gray_r">gist_gray reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
162 <option value="gist_stern_r">gist_stern reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
163 <option value="gist_earth_r">gist_earth reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
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164 <option value="gist_yarg_r">gist_yarg reversed</option>
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165 <option value="gist_ncar_r">gist_ncar reversed</option>
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166 <option value="gist_rainbow_r">gist_rainbow reversed</option>
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167 <option value="gist_heat_r">gist_heat reversed</option>
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168 <option value="gnuplot_r">gnuplot reversed</option>
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169 <option value="gnuplot2_r">gnuplot2 reversed</option>
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170 <option value="CMRmap_r">CMRmap reversed</option>
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171 <option value="bwr_r">bwr reversed</option>
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172 <option value="hsv_r">hsv reversed</option>
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173 <option value="brg_r">brg reversed</option>
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174 <option value="jet_r">jet reversed</option>
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175 <option value="afmhot_r">afmhot reversed</option>
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176 </param>
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177 </xml>
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178
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179
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180 <xml name="multiple_input_matrices">
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181 <repeat name="input_files" title="HiC Matrix files" min="2">
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182 <param name="matrix" type="data" format="h5"
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183 label="HiC Matrix file"
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184 help=""/>
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185 <param name="mlabel" type="text" size="30" optional="true" value=""
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186 label="Label"
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187 help="Label to use in the output. If not given the dataset name will be used instead."/>
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188 </repeat>
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189 </xml>
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190
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191 <token name="@multiple_input_matrices@">
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192 #set $matrices = []
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193 #set $mlabels = []
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194 #for $counter, $i in enumerate($input_files):
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195 ln -s $i.matrix #echo str($counter)+'.npz.h5'#;
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196 #silent $matrices.append( '%s.npz.h5' % $counter )
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197
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198 #if str($i.mlabel.value) != "":
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199 #set $mlabels += ['"%s"' % ($i.mlabel.value)]
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200 #else
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201 #set $mlabels += ['"%s"' % ($i.matrix.name)]
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202 #end if
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203 #end for
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204 #set $mlabels = ' '.join($mlabels)
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205 #set $matrices = ' '.join($matrices)
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206 </token>
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207
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208
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209 <xml name="region">
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210 <param name="region" type="text" label="Region of the genome to limit the operation"
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211 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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212 </xml>
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213
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214
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215
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216 <xml name="kmeans_clustering">
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217 <conditional name="used_multiple_regions">
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218 <param name="used_multiple_regions_options" type="select"
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219 label="Did you compute the matrix with more than one groups of regions?"
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220 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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221 <option value="yes">Yes, I used multiple groups of regions</option>
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222 <option value="no">No, I used only one group</option>
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223 </param>
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224 <when value="no">
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225 <conditional name="clustering">
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226 <param name="clustering_options" type="select" label="Clustering algorithm">
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227 <option value="none">No clustering</option>
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228 <option value="kmeans">Kmeans clustering</option>
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229 </param>
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230 <when value="kmeans">
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231 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
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232 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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233 </when>
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234 <when value="none" />
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235 </conditional>
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236 </when>
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237 <when value="yes" />
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238 </conditional>
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239 </xml>
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240
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241 <token name="@KMEANS_CLUSTERING@">
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242 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
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243 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
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244 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
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245 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
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246 #end if
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247 #end if
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248 #end if
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249 </token>
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250
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251 <xml name="samFlag">
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252 <param name="samFlag" type="integer" optional="true" value=""
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253 label="Filter reads based on the SAM flag"
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254 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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255 </xml>
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256 <xml name="plotNumbers">
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257 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
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258 label="Plot the correlation value"
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259 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
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260 </xml>
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261 <xml name="doNotExtendPairedEnds">
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262 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
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263 label="Do not extend paired ends"
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264 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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265 </xml>
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266
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267 <xml name="ignoreDuplicates">
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268 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
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269 label="Ignore duplicates"
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270 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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271 </xml>
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272
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273 <xml name="minMappingQuality">
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274 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1"
0
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275 label="Minimum mapping quality"
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276 help= "If set, only reads that have a mapping quality score higher than the given value are considered.
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277 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
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278 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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279 </xml>
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280
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281 <xml name="skipZeros">
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282 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
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283 label ="Skip zeros"
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284 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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285 </xml>
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286
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287 <xml name="fragmentLength">
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288 <param name="fragmentLength" type="integer" value="300" min="1"
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289 label="Fragment length used for the sequencing"
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290 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
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291 </xml>
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292
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293 <xml name="scaleFactor">
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294 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
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295 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
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296 </xml>
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297
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298 <xml name="xMax">
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299 <param argument="--xMax" name="xMax" type="integer" optional="true" value=""
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300 label="Max value for the x-axis in counts per bin" />
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301 </xml>
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302
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303 <xml name="filterThreshold">
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304 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"
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305 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/>
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306
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307 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"
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308 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>
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309 </xml>
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310
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311
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312 <xml name="pseudocount">
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313 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
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314 </xml>
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315
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316 <token name="@REFERENCES@">
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317
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318 .. class:: infomark
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319
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320 For more information on the tools, please visit our `help site`_.
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321
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322 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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323
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324 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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325
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326 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
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327 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
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328 .. _help site: https://github.com/fidelram/deepTools/wiki/
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329
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330 </token>
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331
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332
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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333 <xml name="multiple_input_bams">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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334 <repeat name="input_files" title="BAM files" min="2">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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335 <param name="bamfile" type="data" format="bam"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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336 label="Bam file"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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337 help="The BAM file must be sorted."/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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338 <param name="label" type="text" size="30" optional="true" value=""
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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339 label="Label"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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340 help="Label to use in the output. If not given the dataset name will be used instead."/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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341 </repeat>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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342 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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343
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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344 <xml name="multiple_input_bigwigs">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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345 <repeat name="input_files" title="BigWig files" min="2">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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346 <param name="bigwigfile" type="data" format="bigwig"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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347 label="Bigwig file"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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348 help="The Bigwig file must be sorted."/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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349 <param name="label" type="text" size="30" optional="true" value=""
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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350 label="Label"
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351 help="Label to use in the output. If not given the dataset name will be used instead."/>
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352 </repeat>
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353 </xml>
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354
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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355 <xml name="plotTitle">
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356 <param name="plotTitle" type="text" value="" size="30" optional="True"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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357 label="Title of the plot"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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358 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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359 </xml>
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360
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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361 <token name="@multiple_input_bams@">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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362 #import tempfile
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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363 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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364 #set files=[]
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365 #set labels=[]
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366 #for $i in $input_files:
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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367 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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368 #set $temp_input_path = $temp_input_handle.name
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369 #silent $temp_input_handle.close()
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370 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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371 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
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372 #silent $files.append('%s.bam' % $temp_input_path)
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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373
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374 ##set $files += [str($i.bamfile)]
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375 #if str($i.label.value) != "":
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376 #set $labels += ["\"%s\"" % ($i.label.value)]
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377 #else
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378 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
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379 #end if
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380 #end for
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381 </token>
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382
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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383 <token name="@multiple_input_bigwigs@">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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384 #import tempfile
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385 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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386 #set files=[]
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387 #set labels=[]
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388 #for $i in $input_files:
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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389 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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390 #set $temp_input_path = $temp_input_handle.name
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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391 #silent $temp_input_handle.close()
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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392 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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393 #silent $files.append('%s.bw' % $temp_input_path)
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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394
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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395 ##set $files += [str($i.bigwigfile)]
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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396 #if str($i.label.value) != "":
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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397 #set $labels += ["\"%s\"" % ($i.label.value)]
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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398 #else
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399 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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400 #end if
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401 #end for
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402 </token>
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403
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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404 <xml name="reference_genome_source">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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405 <conditional name="source">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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406 <param name="ref_source" type="select" label="Reference genome">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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407 <option value="cached">locally cached</option>
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408 <option value="history">in your history</option>
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409 </param>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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410 <when value="cached">
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411 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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412 <options from_data_table="deepTools_seqs">
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413 <filter type="sort_by" column="1" />
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414 <validator type="no_options" message="No indexes are available." />
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415 </options>
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416 </param>
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417 </when>
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418 <when value="history">
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419 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
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420 </when>
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421 </conditional>
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422 </xml>
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423
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424 <token name="@reference_genome_source@">
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425 #if $source.ref_source=="history":
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426 --genome $source.input1
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427 #else:
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428 --genome "${source.input1_2bit.fields.path}"
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429 #end if
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430 </token>
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431
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432 <xml name="effectiveGenomeSize">
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433 <conditional name="effectiveGenomeSize">
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434 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
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435 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
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436 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
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437 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
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438 <option value="93260000">ce10 (93260000)</option>
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439 <option value="121400000">dm3 (121400000)</option>
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440 <option value="2451960000" selected="true">hg19 (2451960000)</option>
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441 <option value="2150570000">mm9 (2150570000)</option>
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442 <option value="specific">user specified</option>
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443 </param>
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444 <when value="specific">
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445 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
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446 </when>
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447 <when value="2150570000" />
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448 <when value="2451960000" />
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449 <when value="121400000" />
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450 <when value="93260000" />
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451 </conditional>
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452 </xml>
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453
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454 <xml name="image_file_format">
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455 <param name="outFileFormat" type="select" label="Image file format">
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456 <option value="png" selected="true">png</option>
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457 <option value="pdf">pdf</option>
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458 <option value="svg">svg</option>
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459 <option value="eps">eps</option>
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460 <option value="emf">emf</option>
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461 </param>
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462 </xml>
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463
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464 <xml name="missingDataAsZero">
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465 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
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466 label ="Treat missing data as zero"
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467 help ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />
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468 </xml>
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469
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470 <xml name="input_save_matrix_values">
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471 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
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472 </xml>
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473
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474 <xml name="input_graphic_output_settings">
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475 <conditional name="output" >
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476 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
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477 <option value="no" selected="true">no</option>
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478 <option value="yes">yes</option>
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479 </param>
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480 <when value="no" />
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481 <when value="yes">
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482 <yield />
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483 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
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484 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
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485 </when>
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486 </conditional>
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487 </xml>
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488
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489 <xml name="input_image_file_format">
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490 <param name="outFileFormat" type="select" label="Image file format">
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491 <option value="png" selected="true">png</option>
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492 <option value="pdf">pdf</option>
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493 <option value="svg">svg</option>
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494 <option value="eps">eps</option>
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495 <option value="emf">emf</option>
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496 </param>
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497 </xml>
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498
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499 <xml name="output_image_file_format">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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500 <data format="png" name="outFileName" label="${tool.name} image">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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501 <change_format>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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502 <when input="output.outFileFormat" value="pdf" format="pdf" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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503 <when input="output.outFileFormat" value="svg" format="svg" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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504 <when input="output.outFileFormat" value="eps" format="eps" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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505 <when input="output.outFileFormat" value="emf" format="emf" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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506 </change_format>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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507 </data>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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508 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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509
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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510 <xml name="output_save_matrix_values">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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511 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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512 <filter>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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513 ((
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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514 output['showOutputSettings'] == 'yes' and
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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515 output['saveMatrix'] is True
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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516 ))
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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517 </filter>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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518 </data>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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519 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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520
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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521 <xml name="output_graphic_outputs">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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522 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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523 <filter>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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524 ((
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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525 output['showOutputSettings'] == 'yes' and
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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526 output['saveData'] is True
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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527 ))
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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528 </filter>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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529 </data>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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530 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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531 <filter>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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532 ((
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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533 output['showOutputSettings'] == 'yes' and
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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534 output['saveSortedRegions'] is True
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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535 ))
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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536 </filter>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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537 </data>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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538 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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539
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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540
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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541
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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542 </macros>