annotate hicFindTADs.xml @ 0:aab371aa615e draft

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