comparison hicPlotTADs.xml @ 5:144bf28956a7 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5

4:50502e2beaaa

        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
<![CDATA[
        sed '/^$/d' '$tracks_config' &&
        @BINARY@
            --tracks '$tracks_config'
            #if $region and $region is not None:
                --region '$region'

#end if
#end if
#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_type = hic_matrix
title = $track.track_file_style_conditional.title
#if $track.track_file_style_conditional.depth:
depth = $track.track_file_style_conditional.depth
#end if

                    <option value="vlines_track_option">Vlines track</option>
                    <option value="spacer_option">Spacer</option>
                </param>
                <when value="hic_matrix_option">
                    <expand macro="plot_title" />
                    <expand macro="track_input_h5_macro" />
                    
                    <expand macro="colormap" />
                    <param name="depth" type="integer" value="8000000" optional="True" label="Depth" />
                    <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
                    <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>

                <param name="x_axis_select" value="yes" />
            </conditional>   
            <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="title" value="Kc DpnII (Li et al. 2015)" />
                    <param name="colormap" value="RdYlBu_r" />
                    <param name="depth" value="200000" />
                    <param name="transform" value="log1p" />
                    <param name="boundaries_file" value="domains.bed" />

5:144bf28956a7

        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
<![CDATA[

        sed '/^$/d' '$tracks_config' &&
        @BINARY@
            --tracks '$tracks_config'
            #if $region and $region is not None:
                --region '$region'

#end if
#end if
#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.matrix_h5_cooler
file_type = hic_matrix
title = $track.track_file_style_conditional.title
#if $track.track_file_style_conditional.depth:
depth = $track.track_file_style_conditional.depth
#end if

                    <option value="vlines_track_option">Vlines track</option>
                    <option value="spacer_option">Spacer</option>
                </param>
                <when value="hic_matrix_option">
                    <expand macro="plot_title" />
                    <expand macro="matrix_h5_cooler_macro" />
                    
                    <expand macro="colormap" />
                    <param name="depth" type="integer" value="8000000" optional="True" label="Depth" />
                    <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
                    <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>

                <param name="x_axis_select" value="yes" />
            </conditional>   
            <repeat name="tracks">
                <conditional name="track_file_style_conditional">
                    <param name="track_file_style_selector" value="hic_matrix_option" />
                    <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" />
                    <param name="transform" value="log1p" />
                    <param name="boundaries_file" value="domains.bed" />