diff hicPlotTADs.xml @ 0:5e0a39c5bcf6 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicPlotTADs.xml	Thu Mar 30 02:59:24 2017 -0400
@@ -0,0 +1,307 @@
+<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 detect_errors="aggressive">
+<![CDATA[
+        sed '/^$/d' '$tracks_config' &&
+
+        @BINARY@
+            --tracks '$tracks_config'
+            #if $region and $region is not None:
+                --region '$region'
+            #end if
+            --outFileName plot.svg
+
+]]>
+    </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.
+
+#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):
+[hic_section_$counter]
+
+file = $track.track_input
+
+#if $track.title
+title = $track.title
+#end if
+
+#if $track.colormap and $track.track_input.ext == "h5":
+colormap = $track.colormap
+#end if
+
+#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
+
+#if $track.min_value:
+# auto is possible
+min_value = $track.min_value
+#end if
+
+#if $track.max_value:
+max_value = $track.max_value
+#end if
+
+#if $track.transform
+transform = $track.transform
+#end if
+
+#if $track.boundaries_file:
+boundaries_file = $track.boundaries_file
+#end if
+
+#if $track.x_labels == 'yes':
+x labels = yes
+#end if
+
+#if $track.track_input.ext == "bedgraph":
+#set $columns = len(open(str($track.track_input)).readline().split('\t'))
+#if $columns > 5:
+file_type = bedgraph_matrix
+#else:
+file_type = bedgraph
+#end if
+#elif $track.track_input.ext == "h5":
+file_type = hic_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
+#if $track.show_masked_bins:
+show_masked_bins = $track.show_masked_bins
+#end if
+
+#if $track.show_data_range:
+show data range = $track.show_data_range
+#end if
+
+#if $track.nans_to_zeros:
+nans to zeros = $track.nans_to_zeros
+#end if
+
+## to turn off/on printing of labels
+#if str($track.labels) == 'off'
+labels = off
+#end if
+
+#if $track.global_max_row == 'yes':
+global max row = yes
+#end if
+
+## optional: font size can be given if default are not good
+#if $track.fontsize:
+fontsize = $track.fontsize
+#end if
+
+#if $track.number_of_bins:
+number of bins = $track.number_of_bins
+#end if
+
+#if $track.orientation
+orientation = $track.orientation
+#end if
+
+#if $track.type
+type = $track.type
+#end if
+
+#if $track.gene_rows
+gene rows = $track.gene_rows
+#end if
+
+#if $track.spacer_width:
+[spacer]
+width = $track.spacer_width
+#end if
+
+
+#end for</configfile>
+    </configfiles>
+    <inputs>
+        <expand macro="region" />
+        <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="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"/>
+
+            <param name="transform" type="select" optional="True" label="Plot the transformed value">
+                <option value="log1p">log1p</option>
+                <option value="log">log</option>
+            </param>
+            <param name="show_masked_bins" type="boolean" truevalue="yes" falsevalue="no" checked="false"
+                label="Show masked bins" />
+
+            <param name="nans_to_zeros" type="boolean" truevalue="True" falsevalue="False" checked="false"
+                label="NAN's to zeros" />
+
+            <param name="show_data_range" type="boolean" truevalue="yes" falsevalue="no" checked="false"
+                label="SHow data range" />
+
+            <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true"
+                label="Plot labels" />
+
+            <param name="x_labels" type="boolean" truevalue="yes" falsevalue="no" checked="false"
+                label="X labels" />
+
+            <param name="global_max_row" type="boolean" truevalue="yes" falsevalue="no" checked="false"
+                label="Global max rows" />
+
+            <param name="orientation" type="select" optional="True" label="Orientation">
+                <option value="inverted">Inverted</option>
+            </param>
+
+            <param name="display" type="select" optional="True" label="Display type">
+                <option value="collapsed">collapsed</option>
+                <option value="domain">domain</option>
+                <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>
+
+            <param name="depth" type="integer" value="8000000" optional="True" label="Depth" />
+            <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />
+
+            <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
+            <param name="gene_rows" type="integer" value="" optional="True" label="Gene rows" />
+
+            <param name="spacer_width" type="float" value="" optional="True"
+                label="Include spacer at the end of the track." help="Width of the spacer." />
+
+        </repeat>
+
+        <conditional name="x_axis">
+            <param name="x_axis_select" type="select" label="Configure x-axis">
+                <option value="no" selected="True">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="yes">
+                <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
+                <param name="where" type="select" optional="True" label="Where to place the x-axis">
+                    <option value="top">Top</option>
+                    <option value="bottom">Bottom</option>
+                </param>
+            </when>
+            <when value="no" />
+        </conditional>
+
+    </inputs>
+    <outputs>
+        <data name="outFileName" from_work_dir="plot.svg" format="svg"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="region" value="chrX:3000000-3500000"/>
+            <repeat name="tracks">
+                <param name="track_input" 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"/>
+                <param name="spacer_width" value="0.5"/>
+            </repeat>
+            <repeat name="tracks">
+                <param name="track_input" value="tad_classification.bed" ftype="bed" />
+                <param name="title" value="TAD state"/>
+                <param name="width" value="0.5"/>
+                <param name="display" value="collapsed"/>
+                <param name="labels" value="off"/>
+            </repeat>
+            <repeat name="tracks">
+                <param name="track_input" value="tad_score.gz" ftype="bedgraph" />
+                <param name="title" value="TAD separation score (Ramirez et al.)"/>
+                <param name="width" value="10"/>
+                <param name="type" value="lines"/>
+                <param name="spacer_width" value="1"/>
+            </repeat>
+            <repeat name="tracks">
+                <param name="track_input" value="dm3_genes.bed.gz" ftype="bed" />
+                <param name="title" value="genes"/>
+                <param name="width" value="5"/>
+                <param name="fontsize" value="10"/>
+                <param name="spacer_width" value="1"/>
+            </repeat>
+            <repeat name="tracks">
+                <param name="track_input" value="dm3_genes.bed.gz" ftype="bed" />
+                <param name="title" value="max num rows 3"/>
+                <param name="width" value="3"/>
+                <param name="fontsize" value="8"/>
+                <param name="gene_rows" value="3"/>
+                <param name="spacer_width" value="1"/>
+            </repeat>
+            <repeat name="tracks">
+                <param name="track_input" value="dm3_genes.bed6.gz" ftype="bed" />
+                <param name="title" value="bed6 global max row"/>
+                <param name="width" value="20"/>
+                <param name="fontsize" value="10"/>
+                <param name="global_max_row" value="True"/>
+            </repeat>
+            <repeat name="tracks">
+                <param name="track_input" value="domains.bed" ftype="bed" />
+                <param name="type" value="vlines"/>
+            </repeat>
+            <output name="outFileName" file="hicPlotTADs_result1.svg" ftype="svg" compare="sim_size" delta="35000"/>
+        </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>