Mercurial > repos > bgruening > hicexplorer_hicplottads

comparison hicPlotTADs.xml @ 5:144bf28956a7 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
author bgruening
date Sat, 30 Dec 2017 09:34:14 -0500
parents 50502e2beaaa
children 94fff1a6a899
comparison
equal deleted inserted replaced
4:50502e2beaaa 5:144bf28956a7
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"> 8 <command detect_errors="exit_code">
9 <![CDATA[ 9 <![CDATA[
10
10 sed '/^$/d' '$tracks_config' && 11 sed '/^$/d' '$tracks_config' &&
11 @BINARY@ 12 @BINARY@
12 --tracks '$tracks_config' 13 --tracks '$tracks_config'
13 #if $region and $region is not None: 14 #if $region and $region is not None:
14 --region '$region' 15 --region '$region'
29 #end if 30 #end if
30 #end if 31 #end if
31 #for $counter, $track in enumerate($tracks): 32 #for $counter, $track in enumerate($tracks):
32 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": 33 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
33 [hic_section_$counter] 34 [hic_section_$counter]
34 file = $track.track_file_style_conditional.track_input_h5 35 file = $track.track_file_style_conditional.matrix_h5_cooler
35 file_type = hic_matrix 36 file_type = hic_matrix
36 title = $track.track_file_style_conditional.title 37 title = $track.track_file_style_conditional.title
37 #if $track.track_file_style_conditional.depth: 38 #if $track.track_file_style_conditional.depth:
38 depth = $track.track_file_style_conditional.depth 39 depth = $track.track_file_style_conditional.depth
39 #end if 40 #end if
252 <option value="vlines_track_option">Vlines track</option> 253 <option value="vlines_track_option">Vlines track</option>
253 <option value="spacer_option">Spacer</option> 254 <option value="spacer_option">Spacer</option>
254 </param> 255 </param>
255 <when value="hic_matrix_option"> 256 <when value="hic_matrix_option">
256 <expand macro="plot_title" /> 257 <expand macro="plot_title" />
257 <expand macro="track_input_h5_macro" /> 258 <expand macro="matrix_h5_cooler_macro" />
258 259
259 <expand macro="colormap" /> 260 <expand macro="colormap" />
260 <param name="depth" type="integer" value="8000000" optional="True" label="Depth" /> 261 <param name="depth" type="integer" value="8000000" optional="True" label="Depth" />
261 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/> 262 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
262 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/> 263 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
411 <param name="x_axis_select" value="yes" /> 412 <param name="x_axis_select" value="yes" />
412 </conditional> 413 </conditional>
413 <repeat name="tracks"> 414 <repeat name="tracks">
414 <conditional name="track_file_style_conditional"> 415 <conditional name="track_file_style_conditional">
415 <param name="track_file_style_selector" value="hic_matrix_option" /> 416 <param name="track_file_style_selector" value="hic_matrix_option" />
416 <param name="track_input_h5" value="Li_et_al_2015.h5" ftype="h5" /> 417 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
418
417 <param name="title" value="Kc DpnII (Li et al. 2015)" /> 419 <param name="title" value="Kc DpnII (Li et al. 2015)" />
418 <param name="colormap" value="RdYlBu_r" /> 420 <param name="colormap" value="RdYlBu_r" />
419 <param name="depth" value="200000" /> 421 <param name="depth" value="200000" />
420 <param name="transform" value="log1p" /> 422 <param name="transform" value="log1p" />
421 <param name="boundaries_file" value="domains.bed" /> 423 <param name="boundaries_file" value="domains.bed" />