Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

comparison macros.xml @ 8:707f691c974c draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
author bgruening
date Wed, 07 Mar 2018 03:42:32 -0500
parents 30d427846764
children 495ae38f6e0d
comparison
equal deleted inserted replaced
7:be42758f532e 8:707f691c974c
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@">2.0</token> 3 <token name="@WRAPPER_VERSION@">2.1</token>
4
5 <token name="@USE_RANGE@">
6 #if $use_range.select_use_range == "yes_use_range":
7 --range $range_min:$range_max
8 #end if
9 </token>
10
4 <xml name="requirements"> 11 <xml name="requirements">
5 <requirements> 12 <requirements>
6 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement> 13 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
7 <yield /> 14 <yield />
8 </requirements> 15 </requirements>
16 </citations> 23 </citations>
17 </xml> 24 </xml>
18 25
19 <xml name="zMax"> 26 <xml name="zMax">
20 <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow --> 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 -->
28 </xml>
29 <xml name="use_range">
30 <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">
32 <option value="no_use_range">No restriction</option>
33 <option value="yes_use_range">Only consider counts within a range</option>
34 </param>
35 <when value="no_use_range"/>
36 <when value="yes_use_range">
37 <expand macro='range' />
38 </when>
39 </conditional>
40 </xml>
41
42 <xml name="range">
43 <param name="range_min" type="integer" value="" min="0"/>
44 <param name="range_max" type="integer" value="" min="0"/>
21 </xml> 45 </xml>
22 46
23 <xml name="colormap"> 47 <xml name="colormap">
24 <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> 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">
25 <option value="RdYlBu">RdYlBu</option> 49 <option value="RdYlBu">RdYlBu</option>
298 322
299 <xml name="pseudocount"> 323 <xml name="pseudocount">
300 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/> 324 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
301 </xml> 325 </xml>
302 <xml name='matrix_h5_cooler_macro'> 326 <xml name='matrix_h5_cooler_macro'>
303 <param name='matrix_h5_cooler' type="data" format="h5,cool" 327 <param name='matrix_h5_cooler' type="data" format="h5,cool"
304 label="Matrix to compute on."/> 328 label="Matrix to compute on"/>
305
306 </xml> 329 </xml>
307 <xml name='matrix_h5_cooler_multiple_macro'> 330 <xml name='matrix_h5_cooler_multiple_macro'>
308 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" 331 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
309 label="Matrix to compute on." multiple="True"/> 332 label="Matricies to compute on" multiple="true"/>
310 </xml> 333 </xml>
311 <token name="@REFERENCES@"> 334 <token name="@REFERENCES@">
312 335
313 .. class:: infomark 336 .. class:: infomark
314 337
554 <param name="title" type="text" optional="true" label="Plot title"/> 577 <param name="title" type="text" optional="true" label="Plot title"/>
555 </xml> 578 </xml>
556 579
557 <xml name="spacer_macro"> 580 <xml name="spacer_macro">
558 <param name="spacer_width" type="float" value="" optional="True" 581 <param name="spacer_width" type="float" value="" optional="True"
559 label="Include spacer at the end of the track." help="Width of the spacer." /> 582 label="Include spacer at the end of the track." help="Width of the spacer." />
560 </xml> 583 </xml>
561 <xml name="fontsize_macro"> 584 <xml name="fontsize_macro">
562 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> 585 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
563 </xml> 586 </xml>
564 </macros> 587 </macros>