Mercurial > repos > bgruening > hicexplorer_hicdifferentialtad
comparison hicDifferentialTAD.xml @ 0:c852ad97ba28 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
author | bgruening |
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date | Tue, 16 Mar 2021 21:17:26 +0000 |
parents | |
children | 608538d083a2 |
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-1:000000000000 | 0:c852ad97ba28 |
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1 <tool id="hicexplorer_hicdifferentialtad" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> | |
2 <description>searches for differential TADs</description> | |
3 <macros> | |
4 <token name="@BINARY@">hicDifferentialTAD</token> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements" /> | |
8 <command detect_errors="exit_code"><![CDATA[ | |
9 ln -s '$matrix_h5_cooler_target' 'matrix_target.$matrix_h5_cooler_target.ext' && | |
10 ln -s '$matrix_h5_cooler_control' 'matrix_control.$matrix_h5_cooler_control.ext' && | |
11 | |
12 @BINARY@ | |
13 | |
14 --targetMatrix 'matrix_target.$matrix_h5_cooler_target.ext' | |
15 --controlMatrix 'matrix_control.$matrix_h5_cooler_control.ext' | |
16 | |
17 #if $tadDomains: | |
18 --tadDomains '$tadDomains' | |
19 #end if | |
20 | |
21 #if $pValue: | |
22 --pValue $pValue | |
23 #end if | |
24 | |
25 --mode $mode_selector | |
26 --modeReject $modeReject | |
27 --outFileNamePrefix galaxy_differential_tad | |
28 --threads @THREADS@ | |
29 | |
30 ]]> | |
31 </command> | |
32 <inputs> | |
33 <param name='matrix_h5_cooler_target' type="data" format="h5,cool" label="Target matrix to compute on" /> | |
34 <param name='matrix_h5_cooler_control' type="data" format="h5,cool" label="Control matrix to compute on" /> | |
35 | |
36 <param argument="--tadDomains" type="data" format='bed' optional='false' label="TAD domains file" help= "The TADs domain file computed by hicFindTADs." /> | |
37 <param argument="--pValue" type="float" label="P-value" min='0.0' max='1.0' help= "H0 is considered as \'two regions are identical.\' i.e. all regions with a test result of smaller p-value are rejected and considered as differential." value='0.05' /> | |
38 <param name="mode_selector" type="select" label="Method to compute the differentail TAD expression"> | |
39 <option value="intra-TAD">intra-TAD</option> | |
40 <option value="left-inter-TAD">left-inter-TAD</option> | |
41 <option value="right-inter-TAD">right-inter-TAD</option> | |
42 <option value="all" selected="True">all</option> | |
43 </param> | |
44 | |
45 <param name="modeReject" type="select" label="Method to compute the differentail TAD expression"> | |
46 <option value="one" selected="True">one</option> | |
47 <option value="all">all</option> | |
48 </param> | |
49 </inputs> | |
50 <outputs> | |
51 <data name='acceptedTADs' from_work_dir='galaxy_differential_tad_accepted.diff_tad' format='txt' label='Accepted TADs' /> | |
52 <data name='rejectedTADs' from_work_dir='galaxy_differential_tad_rejected.diff_tad' format='txt' label='Rejected TADs' /> | |
53 </outputs> | |
54 <tests> | |
55 <test> | |
56 <param name="matrix_h5_cooler_target" value="small_test_matrix.cool" /> | |
57 <param name="matrix_h5_cooler_control" value="small_test_matrix.cool" /> | |
58 | |
59 <param name="tadDomains" ftype='bed' value="hicDifferentialTAD/multiNone_domains.bed" /> | |
60 <param name="pValue" value="1.0" /> | |
61 <param name="mode_selector" value="all" /> | |
62 <param name="modeReject" value="one" /> | |
63 <output name="acceptedTADs" file="hicDifferentialTAD/accepted.txt" ftype="txt" /> | |
64 <output name="rejectedTADs" file="hicDifferentialTAD/rejected.txt" ftype="txt" /> | |
65 </test> | |
66 </tests> | |
67 <help><![CDATA[ | |
68 | |
69 Differential TAD detection | |
70 ========================== | |
71 | |
72 Computes if precomputed TADs are differentially expressed between two samples. | |
73 | |
74 | |
75 For more information about HiCExplorer please consider our documentation on readthedocs.io_. | |
76 | |
77 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html | |
78 | |
79 ]]> </help> | |
80 <expand macro="citations" /> | |
81 </tool> |