comparison hicPlotTADs.xml @ 1:3615a7c5c119 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f

0:5e0a39c5bcf6

## There are two exceptions for this, the [x-axis] and the [spacer] sections
## that use the secion label to determine the action.

#if $x_axis.x_axis_select == "yes":
[x-axis]
fontsize = $x_axis.fontsize
where = $x_axis.where
#else:
[x-axis]
#end if

#for $counter, $track in enumerate($tracks):

#if $track.color and $track.track_input.ext != "h5":
color = $track.color
#end if

#if $track.depth:
depth = $track.depth
#end if

#if $track.display:
display = $track.display
#end if

##color = black

#if $track.width
width = $track.width
#end if

            <param name="track_input" type="data" format="h5,bed,bedgraph,bigwig,tabular" label="Track file"/>
            <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file"/>
            <param name="title" type="text" optional="true" label="Plot title"/>
            <expand macro="colormap" />
            <param name="color" type="color" value="#000000" label="Track color" optional="True" />
            <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="width" type="float" value="1.5" optional="True" label="Width"/>

                <option value="interlaced">interlaced</option>
            </param>

            <param name="type" type="select" optional="True" label="Plotting type">
                <option value="lines">Lines</option>
                <option value="vlines">vertical dotted lines from the top to the bottom</option>
                <option value="arcplot">arcplot</option>
                <option value="interaction">interaction</option>
                <option value="genes">Genes</option>
            </param>

1:3615a7c5c119

## There are two exceptions for this, the [x-axis] and the [spacer] sections
## that use the secion label to determine the action.

#if $x_axis.x_axis_select == "yes":
[x-axis]
#if $x_axis.fontsize:
fontsize = $x_axis.fontsize
#end if
#if $x_axis.where:
where = $x_axis.where
#end if
#else:
[x-axis]
#end if

#for $counter, $track in enumerate($tracks):

#if $track.color and $track.track_input.ext != "h5":
color = $track.color
#end if

#if $track.border_color:
color = $track.border_color
#end if

#if $track.depth:
depth = $track.depth
#end if

#if $track.display:
display = $track.display
#end if

#if $track.width
width = $track.width
#end if

            <param name="track_input" type="data" format="h5,bed,bedgraph,bigwig,tabular" label="Track file"/>
            <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file"/>
            <param name="title" type="text" optional="true" label="Plot title"/>
            <expand macro="colormap" />
            <param name="color" type="color" value="#000000" label="Track color" optional="True" />
            <param name="border_color" type="color" value="#000000" label="Border color" optional="True" />
            <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="width" type="float" value="1.5" optional="True" label="Width"/>

                <option value="interlaced">interlaced</option>
            </param>

            <param name="type" type="select" optional="True" label="Plotting type">
                <option value="lines">Lines</option>
                <option value="line">Line</option>
                <option value="vlines">vertical dotted lines from the top to the bottom</option>
                <option value="arcplot">arcplot</option>
                <option value="interaction">interaction</option>
                <option value="genes">Genes</option>
            </param>