diff hicInfo.xml @ 0:708e1b8eff5c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicInfo.xml	Mon Dec 16 14:34:49 2019 -0500
@@ -0,0 +1,93 @@
+<tool id="hicexplorer_hicinfo" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>transform a matrix to obs/exp, pearson and covariance matrices</description>
+    <macros>
+        <token name="@BINARY@">hicInfo</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+
+        ln -s '$matrix_h5_cooler' 'matrix_name.$matrix_h5_cooler.ext' &&
+        @BINARY@ --matrices 'matrix_name.$matrix_h5_cooler.ext'
+        -o hicInfo.txt
+]]>
+    </command>
+    <inputs>
+        <expand macro='matrix_h5_cooler_macro' />
+    </inputs>
+    <outputs>
+        <data name="info" from_work_dir="hicInfo.txt" format="txt" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: matrix info"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
+            <output name="info" file="hicInfo/hicInfo_output.txt" ftype="txt" lines_diff="3"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Get information about you Hi-C matrix
+=====================================
+
+This scripts returns useful information about your Hi-C interaction matrix. However, the following information can be included if it is provided by the Hi-C interaction matrix meta data. In case the meta data is missing, the information can be less.
+
+.. code-block:: text
+
+    # Matrix information file. Created with HiCExplorer's hicInfo version 3.2-dev
+    File:	/tmp/tmpyyll1kwi.cool
+    Date:	2019-08-11T19:46:15.959678
+    Genome assembly:	dm3
+    Size:	33,754
+    Bin_length:	5000
+    Number of chromosomes:	15
+    Non-zero elements:	35,857
+    The following columns are available: ['chrom' 'start' 'end']
+
+
+    Generated by:	HiCMatrix-11-dev
+    Cooler library version:	cooler-0.8.5
+    HiCMatrix url:	https://github.com/deeptools/HiCMatrix
+    Interaction matrix created with:	HiCExplorer-3.2-dev
+    URL:	https://github.com/deeptools/HiCExplorer
+
+
+    Build statistics:
+
+    File	/tmp/tmpyyll1kwi.cool		
+    Sequenced reads	99983		
+    Min rest. site distance	300		
+    Max library insert size	1000		
+
+    #	count	(percentage w.r.t. total sequenced reads)
+    Pairs mappable, unique and high quality	52726	(52.73)
+    Hi-C contacts	37321	(37.33)
+    One mate unmapped	8777	(8.78)
+    One mate not unique	3603	(3.60)
+    Low mapping quality	34877	(34.88)
+
+    #	count	(percentage w.r.t. mappable, unique and high quality pairs)
+    dangling end	0	(0.00)
+    self ligation (removed)	0	(0.00)
+    One mate not close to rest site	0	(0.00)
+    same fragment	15393	(29.19)
+    self circle	0	(0.00)
+    duplicated pairs	12	(0.02)
+
+    #	count	(percentage w.r.t. total valid pairs used)
+    inter chromosomal	5955	(15.96)
+    Intra short range (< 20kb)	8853	(23.72)
+    Intra long range (>= 20kb)	22513	(60.32)
+    Read pair type: inward pairs	7145	(19.14)
+    Read pair type: outward pairs	9731	(26.07)
+    Read pair type: left pairs	7156	(19.17)
+    Read pair type: right pairs	7334	(19.65)
+
+
+Please have in mind that the provided information depends on the tool and its version with which the matrix was created.
+
+| For more information about HiCExplorer please consider our documentation on readthedocs.io_
+
+.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
+]]></help>
+    <expand macro="citations" />
+</tool>