Mercurial > repos > bgruening > hicexplorer_hicplottads
diff hicPlotTADs.xml @ 5:144bf28956a7 draft
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 |
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--- a/hicPlotTADs.xml Sat Dec 16 16:36:29 2017 -0500 +++ b/hicPlotTADs.xml Sat Dec 30 09:34:14 2017 -0500 @@ -7,6 +7,7 @@ <expand macro="requirements" /> <command detect_errors="exit_code"> <![CDATA[ + sed '/^$/d' '$tracks_config' && @BINARY@ --tracks '$tracks_config' @@ -31,7 +32,7 @@ #for $counter, $track in enumerate($tracks): #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": [hic_section_$counter] -file = $track.track_file_style_conditional.track_input_h5 +file = $track.track_file_style_conditional.matrix_h5_cooler file_type = hic_matrix title = $track.track_file_style_conditional.title #if $track.track_file_style_conditional.depth: @@ -254,7 +255,7 @@ </param> <when value="hic_matrix_option"> <expand macro="plot_title" /> - <expand macro="track_input_h5_macro" /> + <expand macro="matrix_h5_cooler_macro" /> <expand macro="colormap" /> <param name="depth" type="integer" value="8000000" optional="True" label="Depth" /> @@ -413,7 +414,8 @@ <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="hic_matrix_option" /> - <param name="track_input_h5" value="Li_et_al_2015.h5" ftype="h5" /> + <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/> + <param name="title" value="Kc DpnII (Li et al. 2015)" /> <param name="colormap" value="RdYlBu_r" /> <param name="depth" value="200000" />