Galaxy |

Changeset 8:7e535e3b71f3 (2018-04-27)

Previous changeset 7:94fff1a6a899 (2018-03-07) Next changeset 9:074b3fe3f16e (2018-04-27)

Commit message:
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8

modified:
hicPlotTADs.xml
macros.xml
test-data/compare_matrices_log2ratio.h5
test-data/compare_matrices_pearson_ratio.cool
test-data/covariance_small_50kb.cool
test-data/covariance_small_50kb.h5
test-data/hicCorrectMatrix_result1.npz.h5
test-data/hicMergeMatrixBins_result1.npz.h5
test-data/hicPlotDistVsCounts_result2.png
test-data/hicSumMatrices_result1.npz.h5
test-data/li_viewpoint_32-33Mb.png
test-data/li_viewpoint_32Mb.png
test-data/obs_exp_small_50kb.cool
test-data/obs_exp_small_50kb.h5
test-data/pca1.bw
test-data/pearson_small_50kb.h5
test-data/pearson_small_50kb_transform.cool
test-data/small_matrix_50kb_pearson_pca1_plot.svg
test-data/small_test_matrix_2.h5

removed:
involucro
macros.xml.orig
test-data/multiFDR_zscore_matrix.h5

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

[

b'@@ -1,5 +1,5 @@\n <tool id="hicexplorer_hicplottads" name="@BINARY@" version="@WRAPPER_VERSION@.0">\n- <description>Plots the diagonal, and some values close to the diagonal of a HiC matrix</description>\n+ <description>plot Hi-C contact matrices heatmaps alongside other data tracks</description>\n <macros>\n <token name="@BINARY@">hicPlotTADs</token>\n <import>macros.xml</import>\n@@ -30,7 +30,7 @@\n #end if\n #end if\n #for $counter, $track in enumerate($tracks):\n-#if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": \n+#if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":\n [hic_section_$counter]\n file = $track.track_file_style_conditional.matrix_h5_cooler\n file_type = hic_matrix\n@@ -44,7 +44,7 @@\n #if $track.track_file_style_conditional.min_value:\n min_value = $track.track_file_style_conditional.min_value\n #end if\n-#if $track.track_file_style_conditional.max_value: \n+#if $track.track_file_style_conditional.max_value:\n max_value = $track.track_file_style_conditional.max_value\n #end if\n transform = $track.track_file_style_conditional.transform\n@@ -65,7 +65,7 @@\n scale factor = $track.track_file_style_conditional.scale_factor\n #end if\n \n-#end if \n+#end if\n #if $track.track_file_style_conditional.track_file_style_selector == "tad_score_track_option":\n \n [tad_score_$counter]\n@@ -91,7 +91,7 @@\n file_type = bedgraph\n #end if\n type = lines\n-#end if \n+#end if\n #if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option":\n \n [chrom states_$counter]\n@@ -116,34 +116,34 @@\n title = $track.track_file_style_conditional.title\n #if $track.track_file_style_conditional.color:\n color = $track.track_file_style_conditional.color\n-#end if \n+#end if\n \n #if $track.track_file_style_conditional.width_bed:\n width = $track.track_file_style_conditional.width_bed\n-#end if \n+#end if\n \n #if $track.track_file_style_conditional.labels:\n labels = $track.track_file_style_conditional.labels\n-#end if \n+#end if\n \n #if $track.track_file_style_conditional.type:\n type = $track.track_file_style_conditional.type\n-#end if \n+#end if\n \n file_type = bed\n #if $track.track_file_style_conditional.fontsize:\n fontsize = $track.track_file_style_conditional.fontsize\n-#end if \n+#end if\n \n #if $track.track_file_style_conditional.gene_rows:\n gene rows = $track.track_file_style_conditional.gene_rows\n-#end if \n+#end if\n \n #if $track.track_file_style_conditional.global_max_row:\n global max row = $track.track_file_style_conditional.global_max_row\n-#end if \n+#end if\n \n-#end if \n+#end if\n \n \n #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option":\n@@ -168,7 +168,7 @@\n file_type = bedgraph\n #end if\n type = lines\n-#end if \n+#end if\n \n #if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option":\n \n@@ -195,14 +195,14 @@\n type = fill\n #elif $track.track_file_style_conditional.type_conditional == \'line_option\':\n type = line:$track.track_file_style_conditional.type_conditional.width_line\n-#elif $track.track_file_style_conditional.type_conditional == \'point_option\': \n+#elif $track.track_file_style_conditional.type_conditional == \'point_option\':\n type = points:$track.track_file_style_conditional.type_conditional.width_point\n #end if\n #if $track.track_file_style_conditional.data_range:\n show data range = $track.track_file_style_conditional.data_range\n #end if\n file_type = bigwig\n-#end if \n+#end if\n #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option":\n \n [bedgraph_matrix_$counter]\n@@ -223,21 +223,21 @@\n #end if\n file_type = bedgraph_matrix\n plot horizontal lines=False\n-#end if \n+#end if\n #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option":\n \n [vlines_$counter]\n file = $track.track_file_style_conditional.track_input_bed\n type = vlines\n file_type = bed\n-#end if \n+#end if\n #if $track.track_file_style_conditional.track_file_style_se'..b' <param name="type" value="vlines" />\n- </conditional> \n+ </conditional>\n </repeat>\n <param name="image_file_format" value="png" />\n <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" />\n@@ -587,38 +587,47 @@\n </tests>\n <help><![CDATA[\n \n-Plot TADs\n-=========\n+Plot Topologic Associated Domains\n+=================================\n \n-``hicPlotTADs`` is a visualization tool to plot the topologically associating domains (TADs) in a given region. Additional tracks can be added to enable the comparisons with other data like gene tracks.\n+**hicPlotTADs** is a visualization tool to plot the topologically associating domains (TADs) in a given region. Additional tracks can be added to enable the comparisons with other data like gene, ChIP-seq, RNA-seq or other tracks, including TAD seperation scores computed by ``hicFindTADs``.\n \n-Input\n+_________________\n+\n+Usage\n -----\n-- the region to plot: chr1:1000-2000\n-- the tracks:\n- - the contact matrix\n- - Boundaries file: The result of ``hicFindTADs``.\n-- different tracks for comparison:\n- - Chromatine states: \n- - TAD score\n- - gene tracks\n- - Generic bigwig, bedgraph or bedgraph matrix files\n- - Vlines: vertical lines as a visual support where regions start / end over all tracks\n- - Spacer: Add some space between the different tracks\n+\n+This tool takes various types of tracks as input:\n \n-For each track parameters for the color, the width or the font size can be defined.\n+ - **TAD vizualisation:** corrected Hi-C contact matrix to plot a contact heatmap. It is recommended to follow ``hicPlotMatrix`` instructions. Boundaries file can used, which is the output of ``hicFindTADs`` in bed format. If selected, TADs will be drawn directly on the contact heatmap.\n+ - **Chromatin states:** display blocks of different colors following a bed file.\n+ - **TAD score:** display TAD seperation score computed by ``hicFindTADs``.\n+ - **Gene track / Bed Track:** display genes or bed files. Labels like gene names can be toggled on or off.\n+ - **Bigwig track:** generic bigwig track plotting.\n+ - **Bedgraph track:** generic bedgraph track plotting.\n+ - **Bedgraph matrix track** is used to specifically plot bm files computed by ``hicFindTADs`` (TAD seperation scores).\n+ - **Vlines:** vertical lines drawn on top of all tracks following a bed file. It is used as a visual support where regions start / end over all tracks, for example to display TAD boundaries computed by ``hicFindTADs``.\n+ - **Spacer:** Add some space between two tracks.\n+\n+For each track, parameters for the color, the width or the font size can be defined.\n+\n+_________________\n \n Output\n ------\n-An output looks like this:\n \n+**hicPlotTADs** output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files) also contains Hi-C data. The plot is composed of tracks that need to be specified.\n+Below is represented the 85 Mb to 110 Mb region from human chromosome 2 visualized using **hicPlotTADs**. TADs were computed by ``hicFindTADs``. The additional tracks added correspond to: TAD-separation score (as reported by ``hicFindTADs``), chromatin states, principal component 1 (A/B compartment) computed using ``hicPCA``, ChIP-seq coverage for the H3K27ac mark, DNA methylation, and a gene track. Data are from mouse cardiac myocytes, published by `Nothjunge et al. (2017)`_.\n \n-.. image:: $PATH_TO_IMAGES/master_TADs_plot.png\n- :width: 80 %\n+.. image:: $PATH_TO_IMAGES/hicPlotTADs.png\n+ :width: 70 %\n+\n+_________________\n \n | For more information about HiCExplorer please consider our documentation on readthedocs.io_\n \n .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html\n+.. _`Nothjunge et al. (2017)`: https://www.nature.com/articles/s41467-017-01724-9\n ]]></help>\n <expand macro="citations" />\n </tool>\n'

diff -r 94fff1a6a899 -r 7e535e3b71f3 involucro

Binary file involucro has changed

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 @@
<macros>
     <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
-    <token name="@WRAPPER_VERSION@">2.1</token>
-
+    <token name="@WRAPPER_VERSION@">2.1.2</token>
     <token name="@USE_RANGE@">
         #if $use_range.select_use_range == "yes_use_range":
             --range $range_min:$range_max
@@ -28,7 +27,7 @@
     </xml>
     <xml name="use_range">
         <conditional name="use_range"> 
-            <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range">
+            <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range" help="If given, only counts within the specified range are considered.">
                 <option value="no_use_range">No restriction</option>
                 <option value="yes_use_range">Only consider counts within a range</option>
             </param>
@@ -40,8 +39,8 @@
     </xml>

     <xml name="range">
-        <param name="range_min" type="integer" value="" min="0"/>
-        <param name="range_max" type="integer" value="" min="0"/>
+        <param name='range_min' label="Minimum range to consider interactions" type="integer" value="" min="0" help="The minimum range should be farer from the diagonal than median TAD size in order to reduce background interactions."/>
+        <param name='range_max' label="Maximum range to consider interactions" type="integer" value="" min="0"/>
     </xml>

     <xml name="colormap">
@@ -189,9 +188,9 @@

     <xml name="multiple_input_matrices">
-        <repeat name="input_files" title="HiC Matrix files" min="2">
+        <repeat name="input_files" title="Hi-C Matrix files" min="2">
             <param name="matrix" type="data" format="h5,cool"
-                label="HiC Matrix file"
+                label="Hi-C Matrix file"
                 help=""/>
             <param name="mlabel" type="text" size="30" optional="true" value=""
                 label="Label"

diff -r 94fff1a6a899 -r 7e535e3b71f3 macros.xml.orig
--- a/macros.xml.orig Wed Mar 07 03:46:02 2018 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,585 +0,0 @@\n-<macros>\n- <token name="@THREADS@">\\${GALAXY_SLOTS:-4}</token>\n-<<<<<<< HEAD\n- <token name="@WRAPPER_VERSION@">2.0</token>\n-\n- <token name="@USE_RANGE@">\n- #if $use_range.select_use_range == "yes_use_range":\n- --range $range_min:$range_max\n- #end if\n- </token>\n-\n-=======\n- <token name="@WRAPPER_VERSION@">2.1alpha1</token>\n->>>>>>> joachimwolff-master\n- <xml name="requirements">\n- <requirements>\n- <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>\n- <yield />\n- </requirements>\n- <version_command>@BINARY@ --version</version_command>\n- </xml>\n-\n- <xml name="citations">\n- <citations>\n- <citation type="doi">10.5281/zenodo.1133705</citation>\n- <yield />\n- </citations>\n- </xml>\n-\n- <xml name="zMax">\n- <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> \n- </xml>\n- <xml name="use_range">\n- <conditional name="use_range"> \n- <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range">\n- <option value="no_use_range">No restriction</option>\n- <option value="yes_use_range">Only consider counts within a range</option>\n- </param>\n- <when value="no_use_range"/>\n- <when value="yes_use_range">\n- <param name="range_min" type="integer" value="" min="0"/>\n- <param name="range_max" type="integer" value="" min="0"/>\n- </when>\n- </conditional>\n- </xml>\n- <xml name="colormap">\n- <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">\n- <option value="RdYlBu">RdYlBu</option>\n- <option value="Accent">Accent</option>\n- <option value="Spectral">Spectral</option>\n- <option value="Set1">Set1</option>\n- <option value="Set2">Set2</option>\n- <option value="Set3">Set3</option>\n- <option value="Dark2">Dark2</option>\n- <option value="Reds">Reds</option>\n- <option value="Oranges">Oranges</option>\n- <option value="Greens">Greens</option>\n- <option value="Blues">Blues</option>\n- <option value="Greys">Greys</option>\n- <option value="Purples">Purples</option>\n- <option value="Paired">Paired</option>\n- <option value="Pastel1">Pastel1</option>\n- <option value="Pastel2">Pastel2</option>\n- <option value="spring">spring</option>\n- <option value="summer">summer</option>\n- <option value="autumn">autumn</option>\n- <option value="winter">winter</option>\n- <option value="hot">hot</option>\n- <option value="coolwarm">coolwarm</option>\n- <option value="cool">cool</option>\n- <option value="seismic">seismic</option>\n- <option value="terrain">terrain</option>\n- <option value="ocean">ocean</option>\n- <option value="rainbow">rainbow</option>\n- <option value="bone">bone</option>\n- <option value="flag">flag</option>\n- <option value="prism">prism</option>\n- <option value="cubehelix">cubehelix</option>\n- <option value="binary">binary</option>\n- <option value="pink">pink</option>\n- <option value="gray">gray</option>\n- <option value="copper">copper</option>\n- <option value="BrBG">BrBG</option>\n- <option value="BuGn">BuGn</option>\n- <option value="'..b'/>\n- <when value="yes">\n- <yield />\n- <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>\n- <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>\n- </when>\n- </conditional>\n- </xml>\n-\n- <xml name="input_image_file_format">\n- <param name="outFileFormat" type="select" label="Image file format">\n- <option value="png" selected="true">png</option>\n- <option value="pdf">pdf</option>\n- <option value="svg">svg</option>\n- <option value="eps">eps</option>\n- <option value="emf">emf</option>\n- </param>\n- </xml>\n-\n- <xml name="output_image_file_format">\n- <data format="png" name="outFileName" label="${tool.name} image">\n- <change_format>\n- <when input="output.outFileFormat" value="pdf" format="pdf" />\n- <when input="output.outFileFormat" value="svg" format="svg" />\n- <when input="output.outFileFormat" value="eps" format="eps" />\n- <when input="output.outFileFormat" value="emf" format="emf" />\n- </change_format>\n- </data>\n- </xml>\n-\n- <xml name="output_save_matrix_values">\n- <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">\n- <filter>\n- ((\n- output[\'showOutputSettings\'] == \'yes\' and\n- output[\'saveMatrix\'] is True\n- ))\n- </filter>\n- </data>\n- </xml>\n-\n- <xml name="output_graphic_outputs">\n- <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">\n- <filter>\n- ((\n- output[\'showOutputSettings\'] == \'yes\' and\n- output[\'saveData\'] is True\n- ))\n- </filter>\n- </data>\n- <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">\n- <filter>\n- ((\n- output[\'showOutputSettings\'] == \'yes\' and\n- output[\'saveSortedRegions\'] is True\n- ))\n- </filter>\n- </data>\n- </xml>\n-\n- <xml name="track_input_h5_macro">\n- <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>\n- </xml>\n- <xml name="track_input_bed_macro">\n- <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>\n- </xml>\n- <xml name="track_input_bedgraph_macro">\n- <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>\n- </xml>\n- <xml name="track_input_bigwig_macro">\n- <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>\n- </xml>\n- <xml name="track_input_bedgraph_matrix_macro">\n- <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>\n- </xml>\n- <xml name="track_input_tabular_macro">\n- <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>\n- </xml>\n- <xml name="plot_title">\n- <param name="title" type="text" optional="true" label="Plot title"/>\n- </xml>\n-\n- <xml name="spacer_macro">\n- <param name="spacer_width" type="float" value="" optional="True"\n- label="Include spacer at the end of the track." help="Width of the spacer." />\n- </xml>\n- <xml name="fontsize_macro">\n- <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />\n- </xml>\n-</macros>\n'

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Binary file test-data/pca1.bw has changed

diff -r 94fff1a6a899 -r 7e535e3b71f3 test-data/pearson_small_50kb.h5

Binary file test-data/pearson_small_50kb.h5 has changed

diff -r 94fff1a6a899 -r 7e535e3b71f3 test-data/pearson_small_50kb_transform.cool

Binary file test-data/pearson_small_50kb_transform.cool has changed

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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diff -r 94fff1a6a899 -r 7e535e3b71f3 test-data/small_test_matrix_2.h5

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