Mercurial > repos > bgruening > hicexplorer_hicfindtads

comparison hicFindTADs.xml @ 1:138b5060bc48 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
author bgruening
date Wed, 29 Mar 2017 18:49:21 -0400
parents 40f067ea70e2
children 0b4f8cec3441
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0:40f067ea70e2 1:138b5060bc48
8 <command><![CDATA[ 8 <command><![CDATA[
9 #if $mode.mode_selector == 'TAD_score': 9 #if $mode.mode_selector == 'TAD_score':
10 ln -s '$mode.matrix' matrix.npz.h5 && 10 ln -s '$mode.matrix' matrix.npz.h5 &&
11 #end if 11 #end if
12 12
13 #if $mode.mode_selector == 'find_TADs':
14 ln -s '$tad_score_zscore_matrix' ./tadScoreFile.tabular_zscore_matrix.h5 &&
15 #end if
16
13 hicFindTADs 17 hicFindTADs
14 $mode.mode_selector 18 $mode.mode_selector
15 19
16 #if $mode.mode_selector == 'find_TADs': 20 #if $mode.mode_selector == 'find_TADs':
17 --tadScoreFile '$tadScoreFile' 21 --tadScoreFile '$tadScoreFile'
18 --outPrefix galaxy_tad_prefix 22 --outPrefix galaxy_tad_prefix
19 --maxThreshold $mode.maxThreshold 23 ##--maxThreshold $mode.maxThreshold
20 --delta $mode.delta 24 --delta $mode.delta
21 --lookahead $mode.lookahead 25 --pvalue $mode.pvalue
26 #if $mode.minBoundaryDistance:
27 --minBoundaryDistance $mode.minBoundaryDistance
28 #end if
29
22 #else: 30 #else:
23 --matrix matrix.npz.h5 31 --matrix matrix.npz.h5
24 --maxDepth $mode.maxDepth 32 --maxDepth $mode.maxDepth
25 --minDepth $mode.minDepth 33 --minDepth $mode.minDepth
26 --outFileName ./tadScoreFile.tabular 34 --outFileName ./tadScoreFile.tabular
27 $mode.useLogValues 35
28 --step $mode.step 36 --step $mode.step
29 #end if 37 #end if
30 38
31 ]]></command> 39 ]]></command>
32 <inputs> 40 <inputs>
36 <option value="find_TADs">find TADs</option> 44 <option value="find_TADs">find TADs</option>
37 <option value="TAD_score">TAD score</option> 45 <option value="TAD_score">TAD score</option>
38 </param> 46 </param>
39 <when value="find_TADs"> 47 <when value="find_TADs">
40 <param argument="--tadScoreFile" type="data" format="tabular" label="TAD score file"/> 48 <param argument="--tadScoreFile" type="data" format="tabular" label="TAD score file"/>
41 <param argument="--maxThreshold" type="float" value="0.3" optional="True" label="Only call boundaries that have an score below this threshold"/> 49 <param name="tad_score_zscore_matrix" type="data" format="h5" label="TAD score Matrix file"/>
42 50
43 <param argument="--delta" type="float" value="0.001" optional="True" label="Minimum difference between a peak and followingpoints"/> 51 <param argument="--delta" type="float" value="0.001" optional="True"
44 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."
45 <param argument="--lookahead" type="integer" value="2" optional="True" 53 help="The delta value reduces spurious boundaries that are shallow, which usually
46 label="Number of bins ahead to look for before deciding if a local minimum is a boundary.points"/> 54 occur at the center of large TADs when the TAD-sep. score is flat. Higher
47 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. "/>
48 67
49 </when> 68 </when>
50 <when value="TAD_score"> 69 <when value="TAD_score">
51 70
52 <param argument="--matrix" type="data" format="h5" label="Matrix to use"/> 71 <param argument="--matrix" type="data" format="h5" label="Corrected Hi-C matrix to use for the computations"/>
53 <param argument="--minDepth" type="integer" value="20000" 72 <param argument="--minDepth" type="integer" value="30000"
54 label="Window length to be considered left and right of the cut point in bp" 73 label="Minimum window length (in bp) to be considered to the left and to the right of each Hi-C bin."
55 help="This number should be at least 2 times as large as the bin size of the Hi-C matrix."/> 74 help="This number should be at least 3 times as large as the bin size of the Hi-C matrix."/>
56 <param argument="--maxDepth" type="integer" value="60000" 75 <param argument="--maxDepth" type="integer" value="100000"
57 label="Window length to be considered left and right of the cut point in bp" 76 label="Maximum window length (in bp) to be considered to the left and to the right of each Hi-C bin."
58 help="This number should around 6 times as large as the bin size of the Hi-C matrix."/> 77 help="This number should around 6-10 times as large as the bin size of the Hi-C matrix."/>
59 <param argument="--step" type="integer" value="10000" 78 <param argument="--step" type="integer" value="10000"
60 label="Step size when moving from minDepth to maxDepth"/> 79 label="Step size when moving from minDepth to maxDepth"
61 <param argument="--useLogValues" type="boolean" truevalue="--useLogValues" falsevalue="" 80 help="The step size grows exponentially as `maxDeph + (step * int(x)**1.5) for x in [0, 1, ...]`
62 label="If set, the log of the matrix values areused" /> 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"/>
63 </when> 84 </when>
64 </conditional> 85 </conditional>
65 86
66 87
67 </inputs> 88 </inputs>
68 <outputs> 89 <outputs>
69 <data name="outFileName" from_work_dir="tadScoreFile.tabular" format="tabular"> 90 <data name="outFileName" from_work_dir="tadScoreFile.tabular" format="tabular">
70 <filter>mode['mode_selector'] == "TAD_score"</filter> 91 <filter>mode['mode_selector'] == "TAD_score"</filter>
71 </data> 92 </data>
72 <data name="boundaries" from_work_dir="galaxy_tad_prefix_boundaries.bed" format="bed" label="${tool.name} on ${on_string}: Boundary positions"> 93 <data name="tad_score_zscore_matrix" from_work_dir="tadScoreFile.tabular_zscore_matrix.h5" format="h5">
94 <filter>mode['mode_selector'] == "TAD_score"</filter>
95 </data>
96 <data name="boundaries" from_work_dir="galaxy_tad_prefix_boundaries.bed" format="bed"
97 label="${tool.name} on ${on_string}: Boundary positions">
73 <filter>mode['mode_selector'] == "find_TADs"</filter> 98 <filter>mode['mode_selector'] == "find_TADs"</filter>
74 </data> 99 </data>
75 <data name="score" from_work_dir="galaxy_tad_prefix_score.bedgraph" format="bedgraph" label="${tool.name} on ${on_string}: Matrix with multi-scale TAD scores"> 100 <data name="score" from_work_dir="galaxy_tad_prefix_score.bedgraph" format="bedgraph"
101 label="${tool.name} on ${on_string}: Matrix with multi-scale TAD scores">
76 <filter>mode['mode_selector'] == "find_TADs"</filter> 102 <filter>mode['mode_selector'] == "find_TADs"</filter>
77 </data> 103 </data>
78 <data name="domains" from_work_dir="galaxy_tad_prefix_domains.bed" format="bed" label="${tool.name} on ${on_string}: TAD domains"> 104 <data name="domains" from_work_dir="galaxy_tad_prefix_domains.bed" format="bed"
105 label="${tool.name} on ${on_string}: TAD domains">
79 <filter>mode['mode_selector'] == "find_TADs"</filter> 106 <filter>mode['mode_selector'] == "find_TADs"</filter>
80 </data> 107 </data>
81 <data name="boundaries_bin" from_work_dir="galaxy_tad_prefix_boundaries_bin.bed" format="bed" label="${tool.name} on ${on_string}: Linkage information"> 108 <data name="boundaries_bin" from_work_dir="galaxy_tad_prefix_boundaries.gff"
109 format="bed" label="${tool.name} on ${on_string}: Boundary information plus score">
82 <filter>mode['mode_selector'] == "find_TADs"</filter> 110 <filter>mode['mode_selector'] == "find_TADs"</filter>
83 </data> 111 </data>
84 </outputs> 112 </outputs>
85 <tests> 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>
86 <test> 123 <test>
87 <param name="tadScoreFile" value="hicFindTADs_TAD_score.tabular" ftype="tabular"/> 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"/>
88 <param name="mode_selector" value="find_TADs"/> 126 <param name="mode_selector" value="find_TADs"/>
89 <param name="delta" value="0.002"/> 127 <param name="delta" value="0.002"/>
90 <param name="lookahead" value="2"/> 128 <param name="pvalue" value="0.01"/>
91 <param name="maxThreshold" value="0.2"/> 129
92 <output name="boundaries" file="hicFindTADs_find_boundaries.bed" ftype="bed"/> 130 <output name="boundaries" file="hicFindTADs_find_boundaries.bed" ftype="bed"/>
93 <output name="score" file="hicFindTADs_find_score.bedgraph" ftype="bedgraph"/> 131 <output name="score" file="hicFindTADs_find_score.bedgraph" ftype="bedgraph"/>
94 <output name="domains" file="hicFindTADs_find_domains.bed" ftype="bed"/> 132 <output name="domains" file="hicFindTADs_find_domains.bed" ftype="bed"/>
95 <output name="boundaries_bin" file="hicFindTADs_find_boundaries_bin.bed" ftype="bed"/> 133 <output name="boundaries_bin" file="hicFindTADs_find_boundaries.gff" ftype="gff"/>
96 </test> 134 </test-->
97 <test>
98 <param name="matrix" value="hicBuildMatrix_result1.npz.h5" ftype="h5"/>
99 <param name="mode_selector" value="TAD_score"/>
100 <param name="minDepth" value="20000"/>
101 <param name="maxDepth" value="60000"/>
102 <param name="step" value="10000"/>
103 <output name="outFileName" file="hicFindTADs_TAD_score.tabular" ftype="tabular"/>
104 </test>
105 </tests> 135 </tests>
106 <help><![CDATA[ 136 <help><![CDATA[
107 137
108 **What it does** 138 **What it does**
109 139