view hicPlotTADs.xml @ 0:83b1998b0ec6 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty

<tool id="hicexplorer_hicplottads" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>Plots the diagonal, and some values close to the diagonal of a HiC matrix</description>
    <macros>
        <token name="@BINARY@">hicPlotTADs</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
<![CDATA[

        @BINARY@

            --tracks '$tracks_config'
            #if $region and $region is not None:
                --region '$region'
            #end if


            #if $outFileName and $outFileName is not None:
                --outFileName plot.svg
            #end if

]]>
    </command>
    <configfiles>
        <configfile name="tracks_config">
## lines that start with '#' are comment lines
## and are not interpreted by the program
## the different tracks are represented by sections in this file
## each section starts with a header of the form [hic]
## the content of the section label (in the previous example 'hic') is irrelevant for
## plotting and only used to tell the user when something goes wrong.
## There are two exceptions for this, the [x-axis] and the [spacer] sections
## that use the secion label to determine the action.


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

[hic_section_$counter]

file = $track.track_input
title = $track.title
colormap = $track.colorMap
depth = 100000

##color = black
##width = 1.5


## auto is possible
#if not $track.min_value:
min_value = auto
#else:
min_value = $track.min_value
#end if
#if not $track.max_value:
max_value = auto
#else:
max_value = $track.max_value
#end if
transform = $track.transform


##boundaries_file = conductance_vs_hic/boundaries_all.bed
x labels = yes
type = arcplot
type = interaction

##file_type = h5

#if $track.track_input.ext == "bedgraph":
file_type = bedgraph_matrix
#else:
file_type = $track.track_input.ext
#end if

## show masked bins plots as white lines
## those bins that were not used during the correction
## the default is to extend neighboring bins to
## obtain an aesthetically pleasant output
show_masked_bins = $track.show_masked_bins


## to turn off/on printing of labels
labels = $track.plot_lables
## options are 'genes' or 'domains'.
type = $track.type_of_data
## optional: font size can be given if default are not good
fontsize = $track.fontsize

#if $track.orientation
orientation = $track.orientation
#end if

#if $track.plotting_type
type = lines
#end if

#end for

[x-axis]
# optional
fontsize=20
# optional, options are top or bottom
where=top

# to insert a space simple add a
# section title [spacer]
[spacer]
#optional
width = 0.1


        </configfile>
    </configfiles>
    <inputs>
        <expand macro="region" />
        <param name="foo" type="data" format="h5,bed,bedgraph,bigwig,tabular" label="Track file"/>
        <repeat name="tracks" min="1" title="Include tracks in your plot"
            help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph">

            <param name="track_input" type="data" format="h5,bed,bedgraph,bigwig,tabular" label="Track file"/>
            <param name="title" type="text" optional="true" label="Plot title"/>
            <expand macro="colormap" />
            <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="transform" type="select" label="Plot the transformed value">
                <option value="log1p">log1p</option>
                <option selected="True" value="log">log</option>
            </param>
            <param name="show_masked_bins" type="boolean" truevalue="yes" falsevalue="no" checked="false"
                label="Show masked bins" />

            <param name="plot_lables" type="boolean" truevalue="on" falsevalue="off" checked="false"
                label="Plot lables" />

            <param name="type_of_data" type="select" label="Type of data">
                <option selected="True" value="domains">Domains</option>
                <option value="genes">Genes</option>
            </param>

            <param name="orientation" type="select" optional="True" label="Orientation">
                <option value="inverted">Inverted</option>
            </param>

            <param name="plotting_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>
            </param>

            <param name="fontsize" type="integer" value="10" label="Fontsize" />

        </repeat>


    </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="plot.svg" format="svg"/>
    </outputs>
    <tests>
        <test>
            <param name="foo" value="hicCorrectMatrix_result1.npz.h5" ftype="h5" />
            <param name="region" value="chr3LHet"/>
            <repeat name="tracks">
                <param name="tack_input" value="hicCorrectMatrix_result1.npz.h5" ftype="h5" />
                <param name="title" value="plot_tads_test_1"/>
            </repeat>
            <repeat name="tracks">
                <param name="tack_input" value="hicCorrectMatrix_result1.npz.h5" ftype="h5" />
                <param name="title" value="plot_tads_test_1"/>
            </repeat>
            <output name="outFileName" file="hicPlotTADs_result1.png" ftype="png" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[

**What it does**

Plots the diagonal, and some values close to the diagonal of a HiC matrix. The diagonal of the matrix is plotted horizontally for a region.

]]></help>
    <expand macro="citations" />
</tool>