Mercurial > repos > bgruening > hicexplorer_hicfindtads

comparison hicFindTADs.xml @ 0:aab371aa615e draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
author bgruening
date Thu, 30 Mar 2017 03:22:25 -0400
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-1:000000000000 0:aab371aa615e
1 <tool id="hicexplorer_hicfindtads" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>find minimum cuts that correspond to boundaries</description>
3 <macros>
4 <token name="@BINARY@">hicFindTADs</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command><![CDATA[
9 #if $mode.mode_selector == 'TAD_score':
10 ln -s '$mode.matrix' matrix.npz.h5 &&
11 #end if
12
13 #if $mode.mode_selector == 'find_TADs':
14 ln -s '$tad_score_zscore_matrix' ./tadScoreFile.tabular_zscore_matrix.h5 &&
15 #end if
16
17 hicFindTADs
18 $mode.mode_selector
19
20 #if $mode.mode_selector == 'find_TADs':
21 --tadScoreFile '$tadScoreFile'
22 --outPrefix galaxy_tad_prefix
23 ##--maxThreshold $mode.maxThreshold
24 --delta $mode.delta
25 --pvalue $mode.pvalue
26 #if $mode.minBoundaryDistance:
27 --minBoundaryDistance $mode.minBoundaryDistance
28 #end if
29
30 #else:
31 --matrix matrix.npz.h5
32 --maxDepth $mode.maxDepth
33 --minDepth $mode.minDepth
34 --outFileName ./tadScoreFile.tabular
35
36 --step $mode.step
37 #end if
38
39 ]]></command>
40 <inputs>
41
42 <conditional name="mode">
43 <param name="mode_selector" type="select" label="Range restriction (in bp)" argument="--range">
44 <option value="find_TADs">find TADs</option>
45 <option value="TAD_score">TAD score</option>
46 </param>
47 <when value="find_TADs">
48 <param argument="--tadScoreFile" type="data" format="tabular" label="TAD score file"/>
49 <param name="tad_score_zscore_matrix" type="data" format="h5" label="TAD score Matrix file"/>
50
51 <param argument="--delta" type="float" value="0.001" optional="True"
52 label="Minimum threshold of the difference between the TAD-separation score of a putative boundary and the mean of the TAD-sep. score of surrounding bins."
53 help="The delta value reduces spurious boundaries that are shallow, which usually
54 occur at the center of large TADs when the TAD-sep. score is flat. Higher
55 delta threshold values produce more conservative boundary estimations. By
56 default, multiple delta thresholds are saved for the following delta
57 values: 0.001, 0.01, 0.03, 0.05, 0.1. Other single or multiple values
58 can be given."/> <param argument="--pvalue" type="float" value="0.01"
59 label="P-value threshold"
60 help="The probability of a local minima to be a boundary is estimated by comparing the distribution (Wilcoxon ranksum) of the
61 zscores between the left and right regions (diamond) at the local minimum with the matrix zscores for a diamond at
62 --minDepth to the left and a diamond --minDepth to the right.
63 The reported pvalue is the Bonferroni correction all pvalues."/>
64 <param argument="--minBoundaryDistance" type="integer" value="" optional="True"
65 label="Minimum distance between boundaries (in bp)."
66 help="This parameter can be used to reduce spurious boundaries caused by noise. "/>
67
68 </when>
69 <when value="TAD_score">
70
71 <param argument="--matrix" type="data" format="h5" label="Corrected Hi-C matrix to use for the computations"/>
72 <param argument="--minDepth" type="integer" value="30000"
73 label="Minimum window length (in bp) to be considered to the left and to the right of each Hi-C bin."
74 help="This number should be at least 3 times as large as the bin size of the Hi-C matrix."/>
75 <param argument="--maxDepth" type="integer" value="100000"
76 label="Maximum window length (in bp) to be considered to the left and to the right of each Hi-C bin."
77 help="This number should around 6-10 times as large as the bin size of the Hi-C matrix."/>
78 <param argument="--step" type="integer" value="10000"
79 label="Step size when moving from minDepth to maxDepth"
80 help="The step size grows exponentially as `maxDeph + (step * int(x)**1.5) for x in [0, 1, ...]`
81 until it reaches `maxDepth`. For example, selecting step=10,000, minDepth=20,000
82 and maxDepth=150,000 will compute TAD-scores for window sizes:
83 20,000, 30,000, 40,000, 70,000 and 100,000"/>
84 </when>
85 </conditional>
86
87
88 </inputs>
89 <outputs>
90 <data name="outFileName" from_work_dir="tadScoreFile.tabular" format="tabular">
91 <filter>mode['mode_selector'] == "TAD_score"</filter>
92 </data>
93 <data name="tad_score_zscore_matrix" from_work_dir="tadScoreFile.tabular_zscore_matrix.h5" format="h5">
94 <filter>mode['mode_selector'] == "TAD_score"</filter>
95 </data>
96 <data name="boundaries" from_work_dir="galaxy_tad_prefix_boundaries.bed" format="bed"
97 label="${tool.name} on ${on_string}: Boundary positions">
98 <filter>mode['mode_selector'] == "find_TADs"</filter>
99 </data>
100 <data name="score" from_work_dir="galaxy_tad_prefix_score.bedgraph" format="bedgraph"
101 label="${tool.name} on ${on_string}: Matrix with multi-scale TAD scores">
102 <filter>mode['mode_selector'] == "find_TADs"</filter>
103 </data>
104 <data name="domains" from_work_dir="galaxy_tad_prefix_domains.bed" format="bed"
105 label="${tool.name} on ${on_string}: TAD domains">
106 <filter>mode['mode_selector'] == "find_TADs"</filter>
107 </data>
108 <data name="boundaries_bin" from_work_dir="galaxy_tad_prefix_boundaries.gff"
109 format="bed" label="${tool.name} on ${on_string}: Boundary information plus score">
110 <filter>mode['mode_selector'] == "find_TADs"</filter>
111 </data>
112 </outputs>
113 <tests>
114 <!--test>
115 <param name="matrix" value="hicBuildMatrix_result1.h5" ftype="h5"/>
116 <param name="mode_selector" value="TAD_score"/>
117 <param name="minDepth" value="20000"/>
118 <param name="maxDepth" value="60000"/>
119 <param name="step" value="100000"/>
120 <output name="outFileName" file="hicFindTADs_TAD_score.tabular" ftype="tabular"/>
121 <output name="tad_score_zscore_matrix" file="tadScoreFile.tabular_zscore_matrix.h5" ftype="h5" compare="sim_size"/>
122 </test>
123 <test>
124 <param name="tadScoreFile" value="hicFindTADs_TAD_score.tabular" ftype="tabular"/>
125 <param name="tad_score_zscore_matrix" value="tadScoreFile.tabular_zscore_matrix.h5" ftype="h5"/>
126 <param name="mode_selector" value="find_TADs"/>
127 <param name="delta" value="0.002"/>
128 <param name="pvalue" value="0.01"/>
129
130 <output name="boundaries" file="hicFindTADs_find_boundaries.bed" ftype="bed"/>
131 <output name="score" file="hicFindTADs_find_score.bedgraph" ftype="bedgraph"/>
132 <output name="domains" file="hicFindTADs_find_domains.bed" ftype="bed"/>
133 <output name="boundaries_bin" file="hicFindTADs_find_boundaries.gff" ftype="gff"/>
134 </test-->
135 </tests>
136 <help><![CDATA[
137
138 **What it does**
139
140 Uses the graph clustering measure "conductance" to find minimum cuts that correspond to boundaries.
141
142 ]]></help>
143 <expand macro="citations" />
144 </tool>