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comparison macros.xml @ 0:2074627b0f83 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
author iuc
date Sat, 23 Jun 2018 02:28:35 -0400
parents
children c171f2b7d76e
comparison
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-1:000000000000 0:2074627b0f83
1 <macros>
2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
3 <token name="@WRAPPER_VERSION@">2.0</token>
4 <xml name="requirements">
5 <requirements>
6 <requirement type="package" version="@WRAPPER_VERSION@">pygenometracks</requirement>
7 <yield />
8 </requirements>
9 <version_command>@BINARY@ --version</version_command>
10 </xml>
11
12 <xml name="citations">
13 <citations>
14 <citation type="doi">10.5281/zenodo.1133705</citation>
15 <yield />
16 </citations>
17 </xml>
18
19 <xml name="colormap">
20 <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">
21 <option value="RdYlBu">RdYlBu</option>
22 <option value="Accent">Accent</option>
23 <option value="Spectral">Spectral</option>
24 <option value="Set1">Set1</option>
25 <option value="Set2">Set2</option>
26 <option value="Set3">Set3</option>
27 <option value="Dark2">Dark2</option>
28 <option value="Reds">Reds</option>
29 <option value="Oranges">Oranges</option>
30 <option value="Greens">Greens</option>
31 <option value="Blues">Blues</option>
32 <option value="Greys">Greys</option>
33 <option value="Purples">Purples</option>
34 <option value="Paired">Paired</option>
35 <option value="Pastel1">Pastel1</option>
36 <option value="Pastel2">Pastel2</option>
37 <option value="spring">spring</option>
38 <option value="summer">summer</option>
39 <option value="autumn">autumn</option>
40 <option value="winter">winter</option>
41 <option value="hot">hot</option>
42 <option value="coolwarm">coolwarm</option>
43 <option value="cool">cool</option>
44 <option value="seismic">seismic</option>
45 <option value="terrain">terrain</option>
46 <option value="ocean">ocean</option>
47 <option value="rainbow">rainbow</option>
48 <option value="bone">bone</option>
49 <option value="flag">flag</option>
50 <option value="prism">prism</option>
51 <option value="cubehelix">cubehelix</option>
52 <option value="binary">binary</option>
53 <option value="pink">pink</option>
54 <option value="gray">gray</option>
55 <option value="copper">copper</option>
56 <option value="BrBG">BrBG</option>
57 <option value="BuGn">BuGn</option>
58 <option value="BuPu">BuPu</option>
59 <option value="GnBu">GnBu</option>
60 <option value="OrRd">OrRd</option>
61 <option value="PiYG">PiYG</option>
62 <option value="PRGn">PRGn</option>
63 <option value="PuOr">PuOr</option>
64 <option value="PuRd">PuRd</option>
65 <option value="PuBu">PuBu</option>
66 <option value="RdBu">RdBu</option>
67 <option value="RdGy">RdGy</option>
68 <option value="RdPu">RdPu</option>
69 <option value="YlGn">YlGn</option>
70 <option value="PuBuGn">PuBuGn</option>
71 <option value="RdYlGn">RdYlGn</option>
72 <option value="YlGnBu">YlGnBu</option>
73 <option value="YlOrBr">YlOrBr</option>
74 <option value="YlOrRd">YlOrRd</option>
75 <option value="gist_gray">gist_gray</option>
76 <option value="gist_stern">gist_stern</option>
77 <option value="gist_earth">gist_earth</option>
78 <option value="gist_yarg">gist_yarg</option>
79 <option value="gist_ncar">gist_ncar</option>
80 <option value="gist_rainbow">gist_rainbow</option>
81 <option value="gist_heat">gist_heat</option>
82 <option value="gnuplot">gnuplot</option>
83 <option value="gnuplot2">gnuplot2</option>
84 <option value="CMRmap">CMRmap</option>
85 <option value="bwr">bwr</option>
86 <option value="hsv">hsv</option>
87 <option value="brg">brg</option>
88 <option value="jet">jet</option>
89 <option value="afmhot">afmhot</option>
90 <option value="Accent_r">Accent reversed</option>
91 <option value="Spectral_r">Spectral reversed</option>
92 <option value="Set1_r">Set1 reversed</option>
93 <option value="Set2_r">Set2 reversed</option>
94 <option value="Set3_r">Set3 reversed</option>
95 <option value="Dark2_r">Dark2 reversed</option>
96 <option value="Reds_r">Reds reversed</option>
97 <option value="Oranges_r">Oranges reversed</option>
98 <option value="Greens_r">Greens reversed</option>
99 <option value="Blues_r">Blues reversed</option>
100 <option value="Greys_r">Greys reversed</option>
101 <option value="Purples_r">Purples reversed</option>
102 <option value="Paired_r">Paired reversed</option>
103 <option value="Pastel1_r">Pastel1 reversed</option>
104 <option value="Pastel2_r">Pastel2 reversed</option>
105 <option value="spring_r">spring reversed</option>
106 <option value="summer_r">summer reversed</option>
107 <option value="autumn_r">autumn reversed</option>
108 <option value="winter_r">winter reversed</option>
109 <option value="hot_r">hot reversed</option>
110 <option value="coolwarm_r">coolwarm reversed</option>
111 <option value="cool_r">cool reversed</option>
112 <option value="seismic_r">seismic reversed</option>
113 <option value="terrain_r">terrain reversed</option>
114 <option value="ocean_r">ocean reversed</option>
115 <option value="rainbow_r">rainbow reversed</option>
116 <option value="bone_r">bone reversed</option>
117 <option value="flag_r">flag reversed</option>
118 <option value="prism_r">prism reversed</option>
119 <option value="cubehelix_r">cubehelix reversed</option>
120 <option value="binary_r">binary reversed</option>
121 <option value="pink_r">pink reversed</option>
122 <option value="gray_r">gray reversed</option>
123 <option value="copper_r">copper reversed</option>
124 <option value="BrBG_r">BrBG reversed</option>
125 <option value="BuGn_r">BuGn reversed</option>
126 <option value="BuPu_r">BuPu reversed</option>
127 <option value="GnBu_r">GnBu reversed</option>
128 <option value="OrRd_r">OrRd reversed</option>
129 <option value="PiYG_r">PiYG reversed</option>
130 <option value="PRGn_r">PRGn reversed</option>
131 <option value="PuOr_r">PuOr reversed</option>
132 <option value="PuRd_r">PuRd reversed</option>
133 <option value="PuBu_r">PuBu reversed</option>
134 <option value="RdBu_r">RdBu reversed</option>
135 <option value="RdGy_r">RdGy reversed</option>
136 <option value="RdPu_r">RdPu reversed</option>
137 <option value="YlGn_r">YlGn reversed</option>
138 <option value="PuBuGn_r">PuBuGn reversed</option>
139 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
140 <option value="RdYlGn_r">RdYlGn reversed</option>
141 <option value="YlGnBu_r">YlGnBu reversed</option>
142 <option value="YlOrBr_r">YlOrBr reversed</option>
143 <option value="YlOrRd_r">YlOrRd reversed</option>
144 <option value="gist_gray_r">gist_gray reversed</option>
145 <option value="gist_stern_r">gist_stern reversed</option>
146 <option value="gist_earth_r">gist_earth reversed</option>
147 <option value="gist_yarg_r">gist_yarg reversed</option>
148 <option value="gist_ncar_r">gist_ncar reversed</option>
149 <option value="gist_rainbow_r">gist_rainbow reversed</option>
150 <option value="gist_heat_r">gist_heat reversed</option>
151 <option value="gnuplot_r">gnuplot reversed</option>
152 <option value="gnuplot2_r">gnuplot2 reversed</option>
153 <option value="CMRmap_r">CMRmap reversed</option>
154 <option value="bwr_r">bwr reversed</option>
155 <option value="hsv_r">hsv reversed</option>
156 <option value="brg_r">brg reversed</option>
157 <option value="jet_r">jet reversed</option>
158 <option value="afmhot_r">afmhot reversed</option>
159 </param>
160 </xml>
161
162 <xml name="region">
163 <param argument="--region" type="text" label="Region of the genome to limit the operation"
164 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" />
165 </xml>
166
167 <xml name='matrix_h5_cooler_multiple_macro'>
168 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
169 label="Matricies to compute on" multiple="true"/>
170 </xml>
171 <token name="@REFERENCES@">
172
173 .. class:: infomark
174
175 For more information on the tools, please visit our `help site`_.
176
177 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
178
179 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for
180 Immunobiology and Epigenetics`_.
181
182 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
183 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
184 .. _help site: https://github.com/deeptools/pyGenomeTracks
185
186 </token>
187
188 <xml name="track_input_bed_macro">
189 <param name="track_input_bed" type="data" format="bed" label="Track file bed format" multiple='True'/>
190 </xml>
191 <xml name="track_input_bed_single_macro">
192 <param name="track_input_bed_single" type="data" format="bed" label="Track file bed format"/>
193 </xml>
194 <xml name="track_input_bedgraph_macro">
195 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format" multiple='True'/>
196 </xml>
197 <xml name="track_input_bigwig_macro">
198 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format" multiple='True'/>
199 </xml>
200 <xml name="track_input_bedgraph_matrix_macro">
201 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format" multiple='True'/>
202 </xml>
203 <xml name="plot_title">
204 <param name="title" type="text" optional="true" label="Plot title" multiple='True'/>
205 </xml>
206 <xml name="spacer_macro">
207 <param name="spacer_height" type="float" value="" optional="True"
208 label="Include spacer at the end of the track" help="Height of the spacer." />
209 </xml>
210 </macros>