Mercurial > repos > bgruening > hicexplorer_hicmergematrixbins

annotate hicMergeMatrixBins.xml @ 3:2a62d67cab68 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
author iuc
date Sat, 30 Dec 2017 08:22:41 -0500
parents 62e0b9817f77
children 1111999ae668
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
1 <tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@WRAPPER_VERSION@.0">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
2 <description>Merges bins from a Hi-C matrix</description>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
3 <macros>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
4 <token name="@BINARY@">hicMergeMatrixBins</token>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
5 <import>macros.xml</import>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
6 </macros>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
7 <expand macro="requirements" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
9 hicMergeMatrixBins
3
2a62d67cab68 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
iuc
parents: 2
diff changeset
10 --matrix '$matrix_h5_cooler'
0
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
11 --numBins $numBins
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
12 $runningWindow
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
13 --outFileName ./out.npz.h5
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
14
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
15 ]]>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
16 </command>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
17 <inputs>
3
2a62d67cab68 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
iuc
parents: 2
diff changeset
18 <expand macro='matrix_h5_cooler_macro' />
2a62d67cab68 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
iuc
parents: 2
diff changeset
19
0
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
20 <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
21 <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Merge using a running window of length --numBins" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
22 </inputs>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
23 <outputs>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
24 <data name="outFileName" from_work_dir="out.npz.h5" format="h5"/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
25 </outputs>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
26 <tests>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
27 <test>
3
2a62d67cab68 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
iuc
parents: 2
diff changeset
28 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
0
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
29 <param name="numBins" value="5" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
30 <output name="outFileName" file="hicMergeMatrixBins_result1.npz.h5" ftype="h5" compare="sim_size" delta="24000" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
31 </test>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
32 </tests>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
33 <help><![CDATA[
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
34
2
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
35 Change matrix resolution
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
36 ========================
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
37
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
38 ``hicMergeMatrixBins`` is used to decrease the resolution of a matrix. With this tool you can create out of a 100 kb
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
39 contact matrix a 1000 kb one:
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
40
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
41 Number of bins to merge = 10
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
42
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
43 100 kb * 10 = 1000 kb = 1 Mb
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
44
3
2a62d67cab68 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
iuc
parents: 2
diff changeset
45 This functionality is useful especially for plotting. The higher the resolution of an contact matrix is, the more likely it is
2a62d67cab68 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
iuc
parents: 2
diff changeset
46 to run out of memory while plotting. This is caused by the circumstances that we compute internally with a sparse matrices but
2a62d67cab68 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
iuc
parents: 2
diff changeset
47 to plot we need a dense one. Furthermore, the higher the resolution of a matrix the more detailed it is which can make it
2a62d67cab68 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
iuc
parents: 2
diff changeset
48 difficult to interpret, especially if the read depth of the Hi-C data is not high.
2
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
49
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
50 Input
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
51 -----
0
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
52
2
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
53 Parameters
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
54 __________
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
55 - contact matrix to change the resolution on
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
56 - Number of bins to merge
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
57 - running window
0
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
58
2
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
59 Output
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
60 ------
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
61
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
62 A contact matrix with the resolution ``original resolution * number of bins``.
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
63
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
64 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
65
62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 0
diff changeset
66 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
0
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
67 ]]></help>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
68 <expand macro="citations" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff changeset
69 </tool>