Mercurial > repos > bgruening > hicexplorer_hichyperoptdetectloops

annotate hicHyperoptDetectLoops.xml @ 3:409396ea5cf0 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
author iuc
date Mon, 01 Jul 2024 20:02:17 +0000
parents 7f7c6ead2d0d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
409396ea5cf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 2
diff changeset
1 <tool id="hicexplorer_hichyperoptDetectLoops" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
2 <description>optimizes parameters for hicDetectLoops</description>
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
3 <macros>
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
4 <token name="@BINARY@">hicHyperoptDetectLoops</token>
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
5 <import>macros.xml</import>
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
6 </macros>
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
7 <expand macro="requirements" />
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
9 ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
10 @BINARY@
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
11
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
12 --matrix 'matrix.$matrix_h5_cooler.ext'
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
13
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
14 #if '$proteinFile':
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
15 --proteinFile '$proteinFile'
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
16 #end if
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
17
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
18 #if '$maximumNumberOfLoops':
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
19 --maximumNumberOfLoops '$maximumNumberOfLoops'
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
20 #end if
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
21
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
22 #if '$resolution':
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
23 --resolution '$resolution'
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
24 #end if
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
25
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
26 #if '$runs':
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
27 --runs '$runs'
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
28 #end if
2
7f7c6ead2d0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 0
diff changeset
29
7f7c6ead2d0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 0
diff changeset
30 #if not $prefixLoop_selector == 'keep':
7f7c6ead2d0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 0
diff changeset
31 --chrPrefixLoops $prefixLoop_selector
7f7c6ead2d0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 0
diff changeset
32 #end if
0
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
33 --outputFileName hyperopt_result.txt
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
34
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
35 --threads @THREADS@
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
36 ]]>
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
37 </command>
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
38 <inputs>
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
39 <expand macro="matrix_h5_cooler_macro" />
2
7f7c6ead2d0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 0
diff changeset
40 <param argument="--proteinFile" type="data" format="bed" label="Protein peak file in bed format" help= "The protein file to validate the detected loops." />
7f7c6ead2d0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 0
diff changeset
41 <param argument="--maximumNumberOfLoops" type="integer" min="0" max="100000" label="Maximum number of loops" help= "The maximum number of loops that should be used for optimization computation." value="10000" />
7f7c6ead2d0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 0
diff changeset
42 <param argument="--resolution" type="integer" min="0" max="100000000" label="Resolution of the matrix" help="The matrix resolution of the Hi-C interaction matrix." value="10000" />
7f7c6ead2d0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 0
diff changeset
43 <param name="prefixLoop_selector" type="select" label="Add, remove, or keep the chr-prefix of the loop/TAD data">
7f7c6ead2d0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 0
diff changeset
44 <option value="keep" selected="True">Keep</option>
7f7c6ead2d0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 0
diff changeset
45 <option value="add">Add</option>
7f7c6ead2d0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 0
diff changeset
46 <option value="remove">Remove</option>
7f7c6ead2d0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 0
diff changeset
47 </param>
7f7c6ead2d0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 0
diff changeset
48 <param argument="--runs" type="integer" min="2" max="10000" label="Hyperopt runs" help= "The number of iterations hyperopt uses to search for a result" value="100" />
0
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
49 </inputs>
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
50 <outputs>
2
7f7c6ead2d0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 0
diff changeset
51 <data name="hyperopt_result" from_work_dir="hyperopt_result.txt" format="txt" label="Computed parameters for hicDetectLoops" />
0
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
52 </outputs>
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
53 <tests>
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
54 <test>
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
55 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
56 <param name="proteinFile" value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak" />
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
57 <param name="maximumNumberOfLoops" value="5" />
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
58 <param name="resolution" value="2" />
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
59 <param name="runs" value="5" />
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
60 <output name="hyperopt_result" file="hicHyperoptDetectLoops/loops.bedgraph" ftype="txt" compare="sim_size" />
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
61 </test>
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
62 </tests>
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
63 <help><![CDATA[
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
64
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
65 Hyperopt parameter optimization loop detection
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
66 ==============================================
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
67
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
68 Compute with a protein peak data file (bed format) optimal parameters for the loop calling. Useful proteins are e.g. CTCF or cohesin.
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
69
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
70 _________________
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
71
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
72 Usage
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
73 -----
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
74
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
75 A command line example is available below (easily matchable in Galaxy using each field information):
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
76
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
77 ̀`$ hicHyperoptDetectLoops -m matrix.cool -o hyperopt_result.txt --maximumNumberOfLoops 10000 --resolution 10000 --runs 100`
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
78
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
79
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
80 For more information about HiCExplorer please consider our documentation on readthedocs.io_.
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
81
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
82 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
83
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
84 ]]> </help>
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
85 <expand macro="citations" />
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff changeset
86 </tool>