# HG changeset patch
# User iuc
# Date 1524814727 14400
# Node ID 7e535e3b71f3990359c45b1e550e58144b390206
# Parent 94fff1a6a8995bb5e7f3d62d9b6edde2605bda71
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
diff -r 94fff1a6a899 -r 7e535e3b71f3 hicPlotTADs.xml
--- a/hicPlotTADs.xml Wed Mar 07 03:46:02 2018 -0500
+++ b/hicPlotTADs.xml Fri Apr 27 03:38:47 2018 -0400
@@ -1,5 +1,5 @@
- Plots the diagonal, and some values close to the diagonal of a HiC matrix
+ plot Hi-C contact matrices heatmaps alongside other data tracks
hicPlotTADs
macros.xml
@@ -30,7 +30,7 @@
#end if
#end if
#for $counter, $track in enumerate($tracks):
-#if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
+#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
@@ -44,7 +44,7 @@
#if $track.track_file_style_conditional.min_value:
min_value = $track.track_file_style_conditional.min_value
#end if
-#if $track.track_file_style_conditional.max_value:
+#if $track.track_file_style_conditional.max_value:
max_value = $track.track_file_style_conditional.max_value
#end if
transform = $track.track_file_style_conditional.transform
@@ -65,7 +65,7 @@
scale factor = $track.track_file_style_conditional.scale_factor
#end if
-#end if
+#end if
#if $track.track_file_style_conditional.track_file_style_selector == "tad_score_track_option":
[tad_score_$counter]
@@ -91,7 +91,7 @@
file_type = bedgraph
#end if
type = lines
-#end if
+#end if
#if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option":
[chrom states_$counter]
@@ -116,34 +116,34 @@
title = $track.track_file_style_conditional.title
#if $track.track_file_style_conditional.color:
color = $track.track_file_style_conditional.color
-#end if
+#end if
#if $track.track_file_style_conditional.width_bed:
width = $track.track_file_style_conditional.width_bed
-#end if
+#end if
#if $track.track_file_style_conditional.labels:
labels = $track.track_file_style_conditional.labels
-#end if
+#end if
#if $track.track_file_style_conditional.type:
type = $track.track_file_style_conditional.type
-#end if
+#end if
file_type = bed
#if $track.track_file_style_conditional.fontsize:
fontsize = $track.track_file_style_conditional.fontsize
-#end if
+#end if
#if $track.track_file_style_conditional.gene_rows:
gene rows = $track.track_file_style_conditional.gene_rows
-#end if
+#end if
#if $track.track_file_style_conditional.global_max_row:
global max row = $track.track_file_style_conditional.global_max_row
-#end if
+#end if
-#end if
+#end if
#if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option":
@@ -168,7 +168,7 @@
file_type = bedgraph
#end if
type = lines
-#end if
+#end if
#if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option":
@@ -195,14 +195,14 @@
type = fill
#elif $track.track_file_style_conditional.type_conditional == 'line_option':
type = line:$track.track_file_style_conditional.type_conditional.width_line
-#elif $track.track_file_style_conditional.type_conditional == 'point_option':
+#elif $track.track_file_style_conditional.type_conditional == 'point_option':
type = points:$track.track_file_style_conditional.type_conditional.width_point
#end if
#if $track.track_file_style_conditional.data_range:
show data range = $track.track_file_style_conditional.data_range
#end if
file_type = bigwig
-#end if
+#end if
#if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option":
[bedgraph_matrix_$counter]
@@ -223,21 +223,21 @@
#end if
file_type = bedgraph_matrix
plot horizontal lines=False
-#end if
+#end if
#if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option":
[vlines_$counter]
file = $track.track_file_style_conditional.track_input_bed
type = vlines
file_type = bed
-#end if
+#end if
#if $track.track_file_style_conditional.track_file_style_selector == "spacer_option":
[spacer]
#if $track.track_file_style_conditional.spacer_width:
width = $track.track_file_style_conditional.spacer_width
#end if
-#end if
+#end if
#end for
@@ -249,7 +249,7 @@
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label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead
of the matrix set to lines if a heatmap representing the matrix is not wanted"/>
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label="Global max rows" />
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diff -r 94fff1a6a899 -r 7e535e3b71f3 involucro
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diff -r 94fff1a6a899 -r 7e535e3b71f3 macros.xml
--- a/macros.xml Wed Mar 07 03:46:02 2018 -0500
+++ b/macros.xml Fri Apr 27 03:38:47 2018 -0400
@@ -1,7 +1,6 @@
\${GALAXY_SLOTS:-4}
- 2.1
-
+ 2.1.2
#if $use_range.select_use_range == "yes_use_range":
--range $range_min:$range_max
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- \${GALAXY_SLOTS:-4}
-<<<<<<< HEAD
- 2.0
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- #if $use_range.select_use_range == "yes_use_range":
- --range $range_min:$range_max
- #end if
-
-
-=======
- 2.1alpha1
->>>>>>> joachimwolff-master
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- hicexplorer
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- @BINARY@ --version
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- 10.5281/zenodo.1133705
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- #set $matrices = []
- #set $mlabels = []
- #for $counter, $i in enumerate($input_files):
- ln -s $i.matrix #echo str($counter)+'_matrix'#;
- #silent $matrices.append( '%s_matrix' % $counter )
-
- #if str($i.mlabel.value) != "":
- #set $mlabels += ['"%s"' % ($i.mlabel.value)]
- #else
- #set $mlabels += ['"%s"' % ($i.matrix.name)]
- #end if
- #end for
- #set $mlabels = ' '.join($mlabels)
- #set $matrices = ' '.join($matrices)
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- #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
- #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
- #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
- --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
- #end if
- #end if
- #end if
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-.. class:: infomark
-
-For more information on the tools, please visit our `help site`_.
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-If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
-
-This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
-
-.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
-.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
-.. _help site: https://hicexplorer.readthedocs.org
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- #import tempfile
- #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
- #set files=[]
- #set labels=[]
- #for $i in $input_files:
- #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
- #set $temp_input_path = $temp_input_handle.name
- #silent $temp_input_handle.close()
- #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
- #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
- #silent $files.append('%s.bam' % $temp_input_path)
-
- ##set $files += [str($i.bamfile)]
- #if str($i.label.value) != "":
- #set $labels += ["\"%s\"" % ($i.label.value)]
- #else
- #set $labels += ["\"%s\"" % ($i.bamfile.name)]
- #end if
- #end for
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- #import tempfile
- #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
- #set files=[]
- #set labels=[]
- #for $i in $input_files:
- #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
- #set $temp_input_path = $temp_input_handle.name
- #silent $temp_input_handle.close()
- #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
- #silent $files.append('%s.bw' % $temp_input_path)
-
- ##set $files += [str($i.bigwigfile)]
- #if str($i.label.value) != "":
- #set $labels += ["\"%s\"" % ($i.label.value)]
- #else
- #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
- #end if
- #end for
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- #if $source.ref_source=="history":
- --genome $source.input1
- #else:
- --genome "${source.input1_2bit.fields.path}"
- #end if
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diff -r 94fff1a6a899 -r 7e535e3b71f3 test-data/compare_matrices_log2ratio.h5
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diff -r 94fff1a6a899 -r 7e535e3b71f3 test-data/compare_matrices_pearson_ratio.cool
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diff -r 94fff1a6a899 -r 7e535e3b71f3 test-data/multiFDR_zscore_matrix.h5
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diff -r 94fff1a6a899 -r 7e535e3b71f3 test-data/small_matrix_50kb_pearson_pca1_plot.svg
--- a/test-data/small_matrix_50kb_pearson_pca1_plot.svg Wed Mar 07 03:46:02 2018 -0500
+++ b/test-data/small_matrix_50kb_pearson_pca1_plot.svg Fri Apr 27 03:38:47 2018 -0400
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