diff hicPlotSVL.xml @ 2:3a7752b8d2cb draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"

--- a/hicPlotSVL.xml	Wed Feb 05 20:03:49 2020 -0500
+++ b/hicPlotSVL.xml	Wed Mar 11 17:00:23 2020 -0400
@@ -13,7 +13,7 @@
             ln -s '$m' '${counter}_$identifier' &&
         #end for
         #set $m = ' '.join([ '\'%s_%s\'' % ($counter, @ESCAPE_IDENTIFIER_MATRIX@) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
-       
+
         @BINARY@
             --matrices $m
             #if $distance:
@@ -29,10 +29,10 @@
 
             #if $dpi:
                 --dpi $dpi
-            #end if 
+            #end if
             --plotFileName plot.$image_file_format
             --outFileName p_values.txt
-            --outFileNameData ratios.txt 
+            --outFileNameData ratios.txt
             --threads @THREADS@
 
             && mv plot.$image_file_format plot
@@ -51,7 +51,7 @@
             <option value="pdf">pdf</option>
         </param>
     </inputs>
-    <outputs> 
+    <outputs>
         <data name='output_plot' from_work_dir='plot' format='png' label='Plot SVL'>
             <change_format>
                 <when input="image_file_format" value="svg" format="svg" />
@@ -83,7 +83,7 @@
             <output name="output_plot" file="hicPlotSVL/plot.png" ftype="png" compare="sim_size"/>
             <output name="output_p_values" file="hicPlotSVL/p_values.txt" ftype="txt" compare="sim_size"/>
             <output name="output_ratios" file="hicPlotSVL/ratios.txt" ftype="txt" compare="sim_size"/>
-       
+
         </test>
     </tests>
     <help><![CDATA[
@@ -91,7 +91,80 @@
 Short vs long range contacts
 ============================
 
-Computes the ratio of short vs. long range contacts on the given matrices and makes, if two or more matrices are present a differential test between the matrices.
+hicPlotSVL computes the ratio between short range and long range contacts per chromosome independently. Per sample one box plot is created and, 
+if more than one sample is given, the computed ratios are assumed to be one distribution and a Wilcoxon rank-sum test under H0 'distributions are equal' 
+is computed. All used data is written to a third raw data file.
+
+The distance to distinct short and long range contacts can be set via the –distance parameter; for short range the sum for all contacts smaller or equal this distance are computed, for long range contacts all contacts greater this distance.
+
+
+
+Usage
+-----
+
+
+.. code-block:: text
+
+    $ hicPlotSVL -m hmec_10kb.cool nhek_10kb.cool hmec_10kb.cool --distance 2000000 --threads 4 --plotFileName plot.png --outFileName pvalues.txt --outFileNameData rawData.txt
+
+
+This results in three files:
+
+The raw data containing the sums for short range, long range and ratio per sample and chromosome.
+
+
+.. code-block:: text
+
+    # Created with HiCExplorer's hicPlotSVL 3.3
+    # Short range vs long range contacts per chromosome: raw data
+    # Short range contacts: <= 2000000
+    #	hmec_10kb.cool			nhek_10kb.cool			hmec_10kb.cool
+    # Chromosome	Ratio	Sum <= 2000000	Sum > 2000000	Ratio	Sum <= 2000000	Sum > 2000000	Ratio	Sum <= 2000000	Sum > 2000000
+    1	3.0399769346724543	33476834	11012200	2.79740105237572	44262902	15822866	3.0399769346724543	33476834	11012200
+    2	2.7532203542810625	31723954	11522490	2.5007877714355438	47468438	18981394	2.7532203542810625	31723954	11522490
+    3	2.922650759458664	26251027	8981924	2.6235211241878442	39640848	15109788	2.922650759458664	26251027	8981924
+    4	2.7235598858451637	22474680	8251950	2.5572455199457864	37486882	14659086	2.7235598858451637	22474680	8251950
+    5	2.9585962905193712	22716268	7678056	2.752922527526723	35445722	12875670	2.9585962905193712	22716268	7678056
+    6	3.168274165465025	22872690	7219290	2.8602111006131703	33990211	11883812	3.168274165465025	22872690	7219290
+    7	3.1093346580597516	19603416	6304698	2.8021236966788887	29712823	10603680	3.1093346580597516	19603416	6304698
+    8	3.135391026076832	18355087	5854162	2.7964394470859024	28660624	10248970	3.135391026076832	18355087	5854162
+    9	4.1147978383348125	15395763	3741560	3.819940066283481	21994046	5757694	4.1147978383348125	15395763	3741560
+    10	3.448063050802953	17964043	5209894	3.1116673856502253	26270171	8442474	3.448063050802953	17964043	5209894
+    11	3.5924666993070407	18651850	5191934	3.1364875011923035	26240350	8366158	3.5924666993070407	18651850	5191934
+    12	3.6817551043464416	18640866	5063038	3.306662109403207	26101554	7893626	3.6817551043464416	18640866	5063038
+    13	3.476204237522881	11018462	3169682	3.0976674036654805	18922281	6108558	3.476204237522881	11018462	3169682
+    14	3.70550850832778	11164875	3013048	3.6226817463785164	17245704	4760480	3.70550850832778	11164875	3013048
+    15	4.607631079612186	11165313	2423222	4.567998349104569	15273742	3343640	4.607631079612186	11165313	2423222
+    16	4.397874357146307	10745775	2443402	3.890983210350018	14666462	3769346	4.397874357146307	10745775	2443402
+    17	5.809374740402161	12168235	2094586	5.3360710927739285	14154110	2652534	5.809374740402161	12168235	2094586
+    18	3.7647349280938895	9339833	2480874	3.485487446356812	15019063	4309028	3.7647349280938895	9339833	2480874
+    19	6.492239632778196	8466283	1304062	5.774337450385819	9368978	1622520	6.492239632778196	8466283	1304062
+    20	5.542933774973686	8962935	1617002	4.977679877778358	12009479	2412666	5.542933774973686	8962935	1617002
+    21	6.665622315255486	3910374	586648	6.1843701763589225	6554715	1059884	6.665622315255486	3910374	586648
+    22	8.063663557923096	4992327	619114	7.433759425439728	5932928	798106	8.063663557923096	4992327	619114
+    X	2.208752982178897	14424173	6530460	2.3130534357407995	27628734	11944702	2.208752982178897	14424173	6530460
+    Y	4.165021803993573	36294	8714	3.8063291139240505	45105	11850	4.165021803993573	36294	8714
+    MT
+
+
+
+The p-values between the samples:
+
+.. code-block:: text
+
+    # Created with HiCExplorer's hicPlotSVL 3.3
+    # Short range vs long range contacts per chromosome, p-values of each distribution against each other distribution with Wilcoxon rank-sum
+    # Short range contacts: <= 2000000
+    hmec_10kb.cool	nhek_10kb.cool	0.28362036331636575
+    hmec_10kb.cool	hmec_10kb.cool	1.0
+    nhek_10kb.cool	hmec_10kb.cool	0.28362036331636575
+
+
+
+The box plot:
+
+.. image:: $PATH_TO_IMAGES/plot_svl.png
+   :width: 50%
 
 For more information about HiCExplorer please consider our documentation on readthedocs.io_.