Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

comparison hicBuildMatrix.xml @ 4:652fdcbff650 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
author iuc
date Sat, 16 Dec 2017 16:32:57 -0500
parents 2a13bfe5bff2
children 3bc1425f9000
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3:2a13bfe5bff2 4:652fdcbff650
1 <tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>creates a matrix of interactions</description> 2 <description>creates a contact matrix</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicBuildMatrix</token> 4 <token name="@BINARY@">hicBuildMatrix</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" > 7 <expand macro="requirements" >
132 <output name="outFileName" file="small_test_matrix.h5" ftype="h5" compare="sim_size" delta="30000"/> 132 <output name="outFileName" file="small_test_matrix.h5" ftype="h5" compare="sim_size" delta="30000"/>
133 </test> 133 </test>
134 </tests> 134 </tests>
135 <help><![CDATA[ 135 <help><![CDATA[
136 136
137 **What it does** 137 Creation of the contact matrix
138 138 ===============================
139 Creates a matrix of interactions. 139
140 ``hicBuildMatrix`` creates a contact matrix based on Hi-C read pairs. It requires two sam or bam files
141 corresponding to the first and second mates of the paired-end H-C reads. The sam and bam files should
142 not be sorted by position. There are two main options to create the Hi-C contact matrix, either by
143 fixed bin size (eg. 10.000 bp) or by bins of variable restriction fragment size length.
144 ``hicBuildMatrix`` generates a quality control output that can be used to analyze the quality of the Hi-C reads.
145
146 Input
147 -----
148
149 `hicBuildMatrix` is having the following parameters:
150
151 Parameters
152 __________
153
154
155 - two input BAM/SAM files
156 - a bin size
157 - a restriction cut file as an alternative to the bin size
158 - restriction sequence: e.g. HindIII: GATC
159
160
161
162 Output
163 ------
164
165 `hicBuildMatrix` creates as an output:
166 - the contact matrix
167 - a bam file with the accepted alignments
168 - a quality report.
169
170 Example plot
171 -----------------------------------------------------------------
172 .. image:: $PATH_TO_IMAGES/SRR027956.svg
173 :width: 70%
174
175 Contact matrix created with `hicPlotMatrix`.
176
177 Quality report
178 --------------
179
180 The quality report gives you information about:
181
182 - how many pairs were used to build the contact matrix
183 - dangling end pairs: These are reads that start with the restriction site and constitute reads that were digested but no ligated.
184 - same fragment pairs: These are read mates, facing inward, separated by up to 800 bp that do not have a restriction enzyme in between. These read pairs are not valid Hi-C pairs.
185 - self circles: Self circles are defined as pairs within 25kb with 'outward' read orientation
186 - self ligations: These are read pairs with a restriction site in between that are within 800 bp.
187
188 Contact distance:
189 _________________
190 - inter chromosomal
191 - short range < 20 kb
192 - long range
193
194 Read orientation:
195 _________________
196 - inward pairs
197 - outward pairs
198 - left pairs
199 - right pairs
200
201 .. image:: $PATH_TO_IMAGES/hicQC.png
202 :width: 70 %
203
204 | For more information about HiCExplorer please consider our documentation on readthedocs.io_.
205
206 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
207
140 208
141 ]]></help> 209 ]]></help>
142 <expand macro="citations" /> 210 <expand macro="citations" />
143 </tool> 211 </tool>