Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

comparison macros.xml @ 9:495ae38f6e0d draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
author iuc
date Fri, 27 Apr 2018 03:35:56 -0400
parents 707f691c974c
children 4ceaee0043a5
comparison
equal deleted inserted replaced
8:707f691c974c 9:495ae38f6e0d
1 <macros> 1 <macros>
2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> 2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
3 <token name="@WRAPPER_VERSION@">2.1</token> 3 <token name="@WRAPPER_VERSION@">2.1.2</token>
4
5 <token name="@USE_RANGE@"> 4 <token name="@USE_RANGE@">
6 #if $use_range.select_use_range == "yes_use_range": 5 #if $use_range.select_use_range == "yes_use_range":
7 --range $range_min:$range_max 6 --range $range_min:$range_max
8 #end if 7 #end if
9 </token> 8 </token>
26 <xml name="zMax"> 25 <xml name="zMax">
27 <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow --> 26 <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 -->
28 </xml> 27 </xml>
29 <xml name="use_range"> 28 <xml name="use_range">
30 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range --> 29 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
31 <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range"> 30 <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range" help="If given, only counts within the specified range are considered.">
32 <option value="no_use_range">No restriction</option> 31 <option value="no_use_range">No restriction</option>
33 <option value="yes_use_range">Only consider counts within a range</option> 32 <option value="yes_use_range">Only consider counts within a range</option>
34 </param> 33 </param>
35 <when value="no_use_range"/> 34 <when value="no_use_range"/>
36 <when value="yes_use_range"> 35 <when value="yes_use_range">
38 </when> 37 </when>
39 </conditional> 38 </conditional>
40 </xml> 39 </xml>
41 40
42 <xml name="range"> 41 <xml name="range">
43 <param name="range_min" type="integer" value="" min="0"/> 42 <param name='range_min' label="Minimum range to consider interactions" type="integer" value="" min="0" help="The minimum range should be farer from the diagonal than median TAD size in order to reduce background interactions."/>
44 <param name="range_max" type="integer" value="" min="0"/> 43 <param name='range_max' label="Maximum range to consider interactions" type="integer" value="" min="0"/>
45 </xml> 44 </xml>
46 45
47 <xml name="colormap"> 46 <xml name="colormap">
48 <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> 47 <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
49 <option value="RdYlBu">RdYlBu</option> 48 <option value="RdYlBu">RdYlBu</option>
187 </param> 186 </param>
188 </xml> 187 </xml>
189 188
190 189
191 <xml name="multiple_input_matrices"> 190 <xml name="multiple_input_matrices">
192 <repeat name="input_files" title="HiC Matrix files" min="2"> 191 <repeat name="input_files" title="Hi-C Matrix files" min="2">
193 <param name="matrix" type="data" format="h5,cool" 192 <param name="matrix" type="data" format="h5,cool"
194 label="HiC Matrix file" 193 label="Hi-C Matrix file"
195 help=""/> 194 help=""/>
196 <param name="mlabel" type="text" size="30" optional="true" value="" 195 <param name="mlabel" type="text" size="30" optional="true" value=""
197 label="Label" 196 label="Label"
198 help="Label to use in the output. If not given the dataset name will be used instead."/> 197 help="Label to use in the output. If not given the dataset name will be used instead."/>
199 </repeat> 198 </repeat>