Mercurial > repos > sauria > hifive

annotate hifive_macros.xml @ 17:beff3c415f22 draft default tip

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planemo upload for repository https://github.com/bxlab/galaxy_tools/tools/hifive commit 00f5bb3bc367ca8dfddc094b24463af613eaccc6-dirty
author sauria
date Fri, 01 Dec 2017 12:24:14 -0500
parents 1164d73354cb
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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9
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1 <?xml version="1.0"?>
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2 <macros>
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3 <xml name="requirements">
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4 <requirements>
17
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5 <requirement type='package' version="1.5.3">hifive</requirement>
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6 <requirement type='package' version="2.0.0">mpi4py</requirement>
9
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7 <yield/>
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8 </requirements>
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9 </xml>
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10 <token name="@WRAPPER_VERSION@">0.1</token>
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11 <xml name="stdio">
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12 <stdio>
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13 <!-- Anything other than zero is an error -->
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14 <exit_code range="1:"/>
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15 <exit_code range=":-1"/>
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16 <!-- In case the return code has not been set propery check stderr too -->
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17 <regex match="Error:"/>
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18 <regex match="Exception:"/>
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19 </stdio>
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20 </xml>
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21 <token name="@HIC_FEND@">
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22 -B $command.bed
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23 </token>
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24 <xml name="hic_fend_xml">
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25 <!-- Options controlling fend file creation -->
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26 <param format="bed" name="bed" type="data" label="RE Cutsite BED File" optional="False"/>
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27 </xml>
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28 <token name="@HIC_SEQUENCE@">
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29 -i $command.insert
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30 #if str( $command.datafile.format ) == "bam":
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31 #for $bam_file in $command.datafile.paired_bam:
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32 --bam ${bam_file.readend1} ${bam_file.readend2}
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33 #end for
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34 #elif str( $command.datafile.format ) == "mat":
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35 --mat ${command.datafile.mat}
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36 #else:
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37 #for raw_file in $command.datafile.raw_files:
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38 --raw ${raw_file.raw}
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39 #end for
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40 #end if
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41 </token>
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42 <xml name="hic_sequence_xml">
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43 <!-- Options controlling hic sequence data input -->
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44 <conditional name="datafile">
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45 <param name="format" type="select" label="Data Format">
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46 <option value="bam">bam</option>
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47 <option value="mat">mat</option>
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48 <option value="raw">raw</option>
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49 </param>
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50 <when value="bam">
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51 <repeat name="paired_bam" title="Sequencing lane" min="1">
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52 <param format="bam" name="readend1" label="First read end" type="data"/>
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53 <param format="bam" name="readend2" label="Second read end" type="data"/>
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54 </repeat>
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55 </when>
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56 <when value="mat">
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57 <param format="tabular" name="mat" type="data" label="Mat file" optional="False"/>
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58 </when>
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59 <when value="raw">
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60 <repeat name="raw_files" title="Raw file" min="1">
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61 <param format="tabular" name="raw" type="data" label="Raw file" optional="False"/>
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62 </repeat>
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63 </when>
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64 </conditional>
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65 <param type="integer" name="insert" value="500" label="Maximum insert size" optional="False">
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66 <validator type="in_range" min="1"/>
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67 </param>
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68 </xml>
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69 <token name="@HIC_PROJECT@">
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70 -f $command.minint
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71 -j $command.minbin
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72 -n $command.numbin
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73 </token>
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74 <xml name="hic_project_xml">
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75 <!-- Options controlling hic project creation -->
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76 <param type="integer" name="minint" value="20" label="Minimum interactions per fend" optional="False">
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77 <validator type="in_range" min="1"/>
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78 </param>
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79 <param type="integer" name="minbin" value="1000" label="Minimum distance bin cutoff" optional="False">
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80 <validator type="in_range" min="1"/>
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81 </param>
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82 <param type="integer" name="numbin" value="100" label="Number of distance bins" optional="False" help="A value of zero indicates that finding the distance dependence function should be skipped.">
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83 <validator type="in_range" min="0"/>
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84 </param>
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85 </xml>
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86 <token name="@HIC_RANGE@">
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87 -m $command.filtermin
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88 -x $command.filtermax
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89 </token>
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90 <xml name="hic_range_xml">
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91 <!-- Options controlling hic interaction size range limits -->
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92 <param type="integer" name="filtermin" value="1000000" label="Minimum interaction distance" optional="False" help="The minimum interaction distance included for filtering fends and learning correction values.">
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93 <validator type="in_range" min="0"/>
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94 </param>
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95 <param type="integer" name="filtermax" value="0" label="Maximum interaction distance" optional="False" help="The maximum interaction distance included for filtering fends and learning correction values.">
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96 <validator type="in_range" min="0"/>
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97 </param>
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98 </xml>
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99 <token name="@HIC_CHROMOSOMES@">
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100 #if str( $command.chroms ) != "":
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101 -c $command.chroms
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102 #end if
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103 </token>
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104 <xml name="hic_chromosomes_xml">
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105 <!-- Options controlling hic subset selection of chromosomes -->
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106 <param type="text" size="60" name="chroms" value="" label="Included chromosomes" optional="False" help="If a subset of chromosomes are to be used, enter a comma-separated list of chromosome names."/>
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107 </xml>
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108 <token name="@HIC_NORMALIZE@">
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109 $command.analysis.algorithm
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110 #if str( $command.analysis.algorithm ) == "probability" or str( $command.analysis.algorithm ) == "binning-probability":
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111 -b $command.analysis.probiter
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112 -l $command.analysis.step
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113 -g $command.analysis.change
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114 $command.analysis.precalc
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115 #end if
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116 #if str( $command.analysis.algorithm ) == "express" or str( $command.analysis.algorithm ) == "binning-express" :
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117 $command.analysis.removedist
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118 -w $command.analysis.expreads
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119 $command.analysis.binary
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120 -g $command.analysis.change
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121 #if str( $command.analysis.subalgorithm.kr ) == "yes":
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122 -z
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123 #else
11
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124 -e $command.analysis.subalgorithm.expiter
9
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125 #end if
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126 #end if
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127 #if str( $command.analysis.algorithm ) == "binning" or str( $command.analysis.algorithm ) == "binning-express" or str( $command.analysis.algorithm ) == "binning-probability":
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128 -r $command.analysis.biniter
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129 -t $command.analysis.threshold
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130 -y $command.analysis.binreads
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131 -v $command.analysis.model
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132 -s $command.analysis.modelbins
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133 -u $command.analysis.modeltypes
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134 --pseudocounts $command.analysis.pseudo
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135 #end if
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136 </token>
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137 <xml name="hic_normalize_xml">
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138 <!-- Options controlling hic algorithm selection and normalization parameters -->
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139 <conditional name='analysis'>
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140 <param name="algorithm" type="select" label="Learning Algorithm">
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141 <option value="probability">Probability</option>
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142 <option value="express">Express</option>
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143 <option value="binning">Binning</option>
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144 <option value="binning-probability">Binning-Probability</option>
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145 <option value="binning-express">Binning-Express</option>
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146 </param>
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147
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148 <when value="probability">
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149 <param type="integer" name="probiter" value="1000" label="Maximum number of iterations" optional="False">
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150 <validator type="in_range" min="1"/>
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151 </param>
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152 <param type="float" name="change" value="0.0005" label="Parameter change cutoff" optional="False" help="The cutoff for the absolute gradient values such that learning will cease if all values fall below this threshold.">
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153 <validator type="in_range" min="0.00000001"/>
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154 </param>
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155 <param type="float" name="step" value="0.5" label="Learning rate scaling factor" optional="False">
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156 <validator type="in_range" min="0.000001" max="1.0"/>
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157 </param>
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158 <param type="select" name="precalc" label="Precalculate probability corrections from fragment means">
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159 <option value="-p">yes</option>
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160 <option value="">no</option>
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161 </param>
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162 </when>
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163
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164 <when value="express">
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165 <conditional name="subalgorithm">
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166 <param type="select" name="kr" label="Use Knight-Ruiz algorithm." help="This performs an unweighted matrix balancing for learning express corrections.">
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167 <option value="yes">yes</option>
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168 <option value="no">no</option>
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169 </param>
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170 <when value="yes"/>
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171 <when value="no">
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172 <param type="integer" name="expiter" value="1000" label="Number of express iterations" optional="False">
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173 <validator type="in_range" min="1"/>
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174 </param>
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175 </when>
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176 </conditional>
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177 <param type="select" name="removedist" label="Remove estimated distance-dependence prior to learning express corrections.">
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178 <option value="-d">yes</option>
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179 <option value="">no</option>
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180 </param>
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181 <param type="select" name="expreads" label="Reads to use for learning express corrections.">
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182 <option value="cis">cis</option>
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183 <option value="trans">trans</option>
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184 <option value="all">all</option>
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185 </param>
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186 <param type="float" name="change" value="0.0005" label="Parameter change cutoff" optional="False" help="The minimum mean change in fend correction parameter values needed to keep running past 'iterations' number of iterations. If using the Knight-Ruiz algorithm this is the residual cutoff.">
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187 <validator type="in_range" min="0.00000000000001"/>
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188 </param>
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189 <param type="select" name="binary" label="Use binary indicator instead of counts.">
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190 <option value="">no</option>
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191 <option value="-k">yes</option>
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192 </param>
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193 </when>
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194
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195 <when value="binning">
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196 <param type="integer" name="biniter" value="1000" label="Maximum number of binning iterations" optional="False">
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197 <validator type="in_range" min="1"/>
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198 </param>
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199 <param type="float" name="threshold" value="1.0" label="Learning threshold" optional="False"
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200 help="The minimum change needed in the log-likelihood to continue learning binning corrections.">
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201 <validator type="in_range" min="0.000001" max="1.0"/>
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202 </param>
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203 <param type="select" name="binreads" label="Reads to use for learning binning corrections.">
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204 <option value="cis">cis</option>
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205 <option value="trans">trans</option>
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206 <option value="all">all</option>
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207 </param>
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208 <param type="text" size="60" name="model" value="len,distance" label="Model parameters" optional="False" help="A comma-separated list of fragment characteristics to learn corrections for. These can include 'len' and any characteristics included in the fragment bed file.">
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209 <validator type="empty_field" />
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210 </param>
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211 <param type="text" size="60" name="modelbins" value="20,20" label="Number of parameter bins" optional="False" help="A comma-separated list of bins to divide each model parameter into.">
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212 <validator type="empty_field" />
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213 </param>
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214 <param type="text" size="60" name="modeltypes" value="even,even" label="Parameter types" optional="False" help="A comma-separated list of model parameter types. These can be 'even', 'fixed', 'even-const', and 'fixed-const'.">
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215 <validator type="empty_field" />
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216 </param>
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217 <param type="integer" name="pseudo" value="0" label="Number of pseudo-counts" optional="True">
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218 <validator type="in_range" min="0"/>
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219 </param>
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220 </when>
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221
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222 <when value="binning-probability">
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223 <param type="integer" name="biniter" value="1000" label="Maximum number of binning iterations" optional="False">
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224 <validator type="in_range" min="1"/>
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225 </param>
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226 <param type="float" name="threshold" value="1.0" label="Learning threshold" optional="False"
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227 help="The minimum change needed in the log-likelihood to continue learning binning corrections.">
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228 <validator type="in_range" min="0.000001" max="1.0"/>
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229 </param>
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230 <param type="select" name="binreads" label="Reads to use for learning binning corrections.">
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231 <option value="cis">cis</option>
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232 <option value="trans">trans</option>
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233 <option value="all">all</option>
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234 </param>
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235 <param type="text" size="60" name="model" value="len,distance" label="Model parameters" optional="False" help="A comma-separated list of fragment characteristics to learn corrections for. These can include 'len' and any characteristics included in the fragment bed file.">
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236 <validator type="empty_field" />
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237 </param>
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238 <param type="text" size="60" name="modelbins" value="20,20" label="Number of parameter bins" optional="False" help="A comma-separated list of bins to divide each model parameter into.">
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239 <validator type="empty_field" />
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240 </param>
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241 <param type="text" size="60" name="modeltypes" value="even,even" label="Parameter types" optional="False" help="A comma-separated list of model parameter types. These can be 'even', 'fixed', 'even-const', and 'fixed-const'.">
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242 <validator type="empty_field" />
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243 </param>
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244 <param type="integer" name="pseudo" value="0" label="Number of pseudo-counts" optional="True">
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245 <validator type="in_range" min="0"/>
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246 </param>
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247 <param type="integer" name="probiter" value="1000" label="Maximum number of iterations" optional="False">
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248 <validator type="in_range" min="1"/>
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249 </param>
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250 <param type="float" name="change" value="0.0005" label="Parameter change cutoff" optional="False" help="The cutoff for the absolute gradient values such that learning will cease if all values fall below this threshold.">
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251 <validator type="in_range" min="0.00000001"/>
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252 </param>
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253 <param type="float" name="step" value="0.5" label="Learning rate scaling factor" optional="False">
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254 <validator type="in_range" min="0.000001" max="1.0"/>
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255 </param>
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256 <param type="select" name="precalc" label="Precalculate probability corrections from fragment means">
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257 <option value="-p">yes</option>
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258 <option value="">no</option>
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259 </param>
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260 </when>
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261
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262 <when value="binning-express">
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263 <param type="integer" name="biniter" value="1000" label="Maximum number of binning iterations" optional="False">
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264 <validator type="in_range" min="1"/>
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265 </param>
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266 <param type="float" name="threshold" value="1.0" label="Learning threshold" optional="False"
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267 help="The minimum change needed in the log-likelihood to continue learning binning corrections.">
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268 <validator type="in_range" min="0.000001" max="1.0"/>
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269 </param>
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270 <param type="select" name="binreads" label="Reads to use for learning binning corrections.">
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271 <option value="cis">cis</option>
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272 <option value="trans">trans</option>
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273 <option value="all">all</option>
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274 </param>
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275 <param type="text" size="60" name="model" value="len,distance" label="Model parameters" optional="False" help="A comma-separated list of fragment characteristics to learn corrections for. These can include 'len' and any characteristics included in the fragment bed file.">
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276 <validator type="empty_field" />
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277 </param>
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278 <param type="text" size="60" name="modelbins" value="20,20" label="Number of parameter bins" optional="False" help="A comma-separated list of bins to divide each model parameter into.">
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279 <validator type="empty_field" />
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280 </param>
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281 <param type="text" size="60" name="modeltypes" value="even,even" label="Parameter types" optional="False" help="A comma-separated list of model parameter types. These can be 'even', 'fixed', 'even-const', and 'fixed-const'.">
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282 <validator type="empty_field" />
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283 </param>
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284 <param type="integer" name="pseudo" value="0" label="Number of pseudo-counts" optional="True">
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285 <validator type="in_range" min="0"/>
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286 </param>
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287 <param type="integer" name="expiter" value="1000" label="Number of express iterations" optional="False">
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288 <validator type="in_range" min="1"/>
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289 </param>
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290 <param type="select" name="removedist" label="Remove estimated distance-dependence prior to learning express corrections.">
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291 <option value="-d">yes</option>
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292 <option value="">no</option>
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293 </param>
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294 <param type="select" name="expreads" label="Reads to use for learning express corrections.">
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295 <option value="cis">cis</option>
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296 <option value="trans">trans</option>
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297 <option value="all">all</option>
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298 </param>
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299 </when>
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300 </conditional>
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301 </xml>
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302 <token name="@HIC_DATATYPE@">
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303 -d $command.datatype
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304 </token>
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305 <xml name="hic_datatype_xml">
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306 <!-- Options controlling type of hic data to return -->
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307 <param name="datatype" type="select" label="Datatype">
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308 <option value="raw">raw</option>
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309 <option value="fend">fend-corrected</option>
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310 <option value="distance">distance-corrected</option>
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311 <option value="enrichment">enrichment</option>
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312 </param>
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313 </xml>
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314 <token name="@5C_FRAGMENT@">
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315 $command.bed
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316 </token>
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317 <xml name="5c_fragment_xml">
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318 <!-- Options controlling fragment file creation -->
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319 <param format="bed" name="bed" type="data" label="Probed RE fragment boundary BED File" optional="False"/>
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320 </xml>
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321 <token name="@5C_SEQUENCE@">
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322 #if str( $command.datafile.format ) == "bam":
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323 #for $bam_file in $command.datafile.paired_bam:
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324 -B ${bam_file.readend1} ${bam_file.readend2}
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325 #end for
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326 #else:
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327 #for $count_file in $command.datafile.count_files:
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328 -C ${count_file.count}
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329 #end for
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330 #end if
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331 </token>
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332 <xml name="5c_sequence_xml">
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333 <!-- Options controlling 5c sequence data input -->
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334 <conditional name="datafile">
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335 <param name="format" type="select" label="Data Format">
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336 <option value="bam">bam</option>
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337 <option value="count">count</option>
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338 </param>
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339 <when value="bam">
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340 <repeat name="paired_bam" title="Sequencing lane" min="1">
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341 <param format="bam" name="readend1" label="First read end" type="data"/>
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342 <param format="bam" name="readend2" label="Second read end" type="data"/>
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343 </repeat>
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344 </when>
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345 <when value="count">
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346 <repeat name="count_files" title="Counts file" min="1">
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347 <param format="tabular" name="count" type="data" label="Counts file" optional="False"/>
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348 </repeat>
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349 </when>
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350 </conditional>
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351 </xml>
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352 <token name="@5C_PROJECT@">
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353 -f $command.minint
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354 </token>
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355 <xml name="5c_project_xml">
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356 <!-- Options controlling 5c project creation -->
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357 <param type="integer" name="minint" value="20" label="Minimum interactions per fragment" optional="False">
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358 <validator type="in_range" min="1"/>
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359 </param>
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360 </xml>
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361 <token name="@5C_RANGE@">
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362 -m $command.mindist
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363 -x $command.maxdist
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364 </token>
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365 <xml name="5c_range_xml">
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366 <!-- Options controlling 5c interaction size range limits -->
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367 <param type="integer" name="mindist" value="0" label="Minimum interaction distance" optional="False" help="The minimum interaction distance included for filtering fragments and learning correction values.">
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368 <validator type="in_range" min="0"/>
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369 </param>
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370 <param type="integer" name="maxdist" value="0" label="Maximum interaction distance" optional="False" help="The maximum interaction distance included for filtering fragments and learning correction values. A value of zero indicates no upper limit.">
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371 <validator type="in_range" min="0"/>
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372 </param>
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373 </xml>
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374 <token name="@5C_REGIONS@">
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375 #if str( $command.regions ) != "":
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376 -r $command.regions
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377 #end if
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378 </token>
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379 <xml name="5c_regions_xml">
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380 <!-- Options controlling 5c subset selection of regions -->
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381 <param type="text" size="60" name="regions" value="" label="Included regions" optional="False" help="If a subset of regions are to be used, enter a comma-separated list of region indices."/>
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382 </xml>
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383 <token name="@5C_NORMALIZE@">
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384 $command.analysis.algorithm
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385 #if str( $command.analysis.algorithm ) == "probability" or str( $command.analysis.algorithm ) == "binning-probability" or str( $command.analysis.algorithm ) == "probability-binning":
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386 -b $command.analysis.probiter
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387 -l $command.analysis.step
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388 -g $command.analysis.change
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389 $command.analysis.precalc
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390 #end if
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391 #if str( $command.analysis.algorithm ) == "express" or str( $command.analysis.algorithm ) == "binning-express" or str( $command.analysis.algorithm ) == "probability-express":
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392 $command.analysis.removedist
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393 -w $command.analysis.expreads
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394 #if str( $command.analysis.subalgorithm.kr ) == "yes":
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395 -z
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396 #else:
11
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397 -e $command.analysis.subalgorithm.expiter
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398 $command.analysis.subalgorithm.logged
9
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399 #end if
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400 #end if
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401 #if str( $command.analysis.algorithm ) == "binning" or str( $command.analysis.algorithm ) == "binning-express" or str( $command.analysis.algorithm ) == "binning-probability" or str( $command.analysis.algorithm ) == "express-binning" or str( $command.analysis.algorithm ) == "probability-binning":
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402 -i $command.analysis.biniter
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403 -t $command.analysis.threshold
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404 -y $command.analysis.binreads
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405 -v $command.analysis.model
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406 -n $command.analysis.modelbins
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407 -u $command.analysis.modeltypes
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408 #end if
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409 </token>
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410 <xml name="5c_normalize_xml">
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411 <!-- Options controlling 5c algorithm selection and normalization parameters -->
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412 <conditional name='analysis'>
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413 <param name="algorithm" type="select" label="Learning Algorithm">
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414 <option value="probability">Probability</option>
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415 <option value="express">Express</option>
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416 <option value="binning">Binning</option>
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417 <option value="binning-probability">Binning-Probability</option>
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418 <option value="binning-express">Binning-Express</option>
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419 <option value="probability-binning">Probability-Binning</option>
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420 <option value="express-binning">Express-Binning</option>
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421 </param>
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422
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423 <when value="probability">
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424 <param type="integer" name="probiter" value="1000" label="Maximum number of iterations" optional="False">
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425 <validator type="in_range" min="1"/>
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426 </param>
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427 <param type="float" name="change" value="0.0005" label="Parameter change cutoff" optional="False" help="The cutoff for the absolute gradient values such that learning will cease if all values fall below this threshold.">
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428 <validator type="in_range" min="0.00000001"/>
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429 </param>
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430 <param type="float" name="step" value="0.5" label="Learning rate scaling factor" optional="False">
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431 <validator type="in_range" min="0.000001" max="1.0"/>
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432 </param>
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433 <param type="select" name="precalc" label="Precalculate probability corrections from fragment means">
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434 <option value="-p">yes</option>
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435 <option value="">no</option>
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436 </param>
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437 </when>
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438
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439 <when value="express">
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440 <conditional name="subalgorithm">
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441 <param type="select" name="kr" label="Use Knight-Ruiz algorithm." help="This performs an unweighted matrix balancing for learning express corrections.">
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442 <option value="yes">yes</option>
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443 <option value="no">no</option>
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444 </param>
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445 <when value="yes"/>
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446 <when value="no">
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447 <param type="integer" name="expiter" value="1000" label="Number of express iterations" optional="False">
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448 <validator type="in_range" min="1"/>
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diff changeset
449 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
450 <param type="select" name="logged" label="Use logged-reads instead of reads.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
451 <option value="-k">yes</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
452 <option value="">no</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
453 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
454 </when>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
455 </conditional>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
456 <param type="select" name="removedist" label="Remove estimated distance-dependence prior to learning express corrections.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
457 <option value="-d">yes</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
458 <option value="">no</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
459 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
460 <param type="select" name="expreads" label="Reads to use for learning express corrections.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
461 <option value="cis">cis</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
462 <option value="trans">trans</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
463 <option value="all">all</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
464 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
465 </when>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
466
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
467 <when value="binning">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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468 <param type="integer" name="biniter" value="1000" label="Maximum number of binning iterations" optional="False">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
469 <validator type="in_range" min="1"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
470 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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471 <param type="float" name="threshold" value="1.0" label="Learning threshold" optional="False"
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
472 help="The minimum change needed in the log-likelihood to continue learning binning corrections.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
473 <validator type="in_range" min="0.000001" max="1.0"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
474 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
475 <param type="select" name="binreads" label="Reads to use for learning binning corrections.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
476 <option value="cis">cis</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
477 <option value="trans">trans</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
478 <option value="all">all</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
479 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
480 <param type="text" size="60" name="model" value="len" label="Model parameters" optional="False" help="A comma-separated list of fragment characteristics to learn corrections for. These can include 'len' and any characteristics included in the fragment bed file.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
481 <validator type="empty_field" />
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
482 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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483 <param type="text" size="60" name="modelbins" value="10" label="Number of parameter bins" optional="False" help="A comma-separated list of bins to divide each model parameter into.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
484 <validator type="empty_field" />
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
485 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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486 <param type="text" size="60" name="modeltypes" value="even" label="Parameter types" optional="False" help="A comma-separated list of model parameter types. These can be 'even', 'fixed', 'even-const', and 'fixed-const'.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
487 <validator type="empty_field" />
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
488 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
489 </when>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
490
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
491 <when value="binning-probability">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
492 <param type="integer" name="biniter" value="1000" label="Maximum number of binning iterations" optional="False">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
493 <validator type="in_range" min="1"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
494 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
495 <param type="float" name="threshold" value="1.0" label="Learning threshold" optional="False"
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
496 help="The minimum change needed in the log-likelihood to continue learning binning corrections.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
497 <validator type="in_range" min="0.000001" max="1.0"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
498 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
499 <param type="select" name="binreads" label="Reads to use for learning binning corrections.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
500 <option value="cis">cis</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
501 <option value="trans">trans</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
502 <option value="all">all</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
503 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
504 <param type="text" size="60" name="model" value="len" label="Model parameters" optional="False" help="A comma-separated list of fragment characteristics to learn corrections for. These can include 'len' and any characteristics included in the fragment bed file.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
505 <validator type="empty_field" />
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
506 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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507 <param type="text" size="60" name="modelbins" value="10" label="Number of parameter bins" optional="False" help="A comma-separated list of bins to divide each model parameter into.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
508 <validator type="empty_field" />
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
509 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
510 <param type="text" size="60" name="modeltypes" value="even" label="Parameter types" optional="False" help="A comma-separated list of model parameter types. These can be 'even', 'fixed', 'even-const', and 'fixed-const'.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
511 <validator type="empty_field" />
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
512 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
513 <param type="integer" name="probiter" value="1000" label="Maximum number of iterations" optional="False">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
514 <validator type="in_range" min="1"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
515 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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516 <param type="float" name="change" value="0.0005" label="Parameter change cutoff" optional="False" help="The cutoff for the absolute gradient values such that learning will cease if all values fall below this threshold.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
517 <validator type="in_range" min="0.00000001"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
518 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
519 <param type="float" name="step" value="0.5" label="Learning rate scaling factor" optional="False">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
520 <validator type="in_range" min="0.000001" max="1.0"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
521 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
522 <param type="select" name="precalc" label="Precalculate probability corrections from fragment means">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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523 <option value="-p">yes</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
524 <option value="">no</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
525 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
526 </when>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
527
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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528 <when value="binning-express">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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529 <param type="integer" name="biniter" value="1000" label="Maximum number of binning iterations" optional="False">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
530 <validator type="in_range" min="1"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
531 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
532 <param type="float" name="threshold" value="1.0" label="Learning threshold" optional="False"
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
533 help="The minimum change needed in the log-likelihood to continue learning binning corrections.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
534 <validator type="in_range" min="0.000001" max="1.0"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
535 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
536 <param type="select" name="binreads" label="Reads to use for learning binning corrections.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
537 <option value="cis">cis</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
538 <option value="trans">trans</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
539 <option value="all">all</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
540 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
541 <param type="text" size="60" name="model" value="len" label="Model parameters" optional="False" help="A comma-separated list of fragment characteristics to learn corrections for. These can include 'len' and any characteristics included in the fragment bed file.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
542 <validator type="empty_field" />
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
543 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
544 <param type="text" size="60" name="modelbins" value="10" label="Number of parameter bins" optional="False" help="A comma-separated list of bins to divide each model parameter into.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
545 <validator type="empty_field" />
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
546 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
547 <param type="text" size="60" name="modeltypes" value="even" label="Parameter types" optional="False" help="A comma-separated list of model parameter types. These can be 'even', 'fixed', 'even-const', and 'fixed-const'.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
548 <validator type="empty_field" />
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
549 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
550 <param type="integer" name="expiter" value="1000" label="Number of express iterations" optional="False">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
551 <validator type="in_range" min="1"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
552 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
553 <param type="select" name="removedist" label="Remove estimated distance-dependence prior to learning express corrections.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
554 <option value="-d">yes</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
555 <option value="">no</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
556 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
557 <param type="select" name="expreads" label="Reads to use for learning express corrections.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
558 <option value="cis">cis</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
559 <option value="trans">trans</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
560 <option value="all">all</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
561 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
562 </when>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
563
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
564 <when value="probability-binning">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
565 <param type="integer" name="probiter" value="1000" label="Maximum number of iterations" optional="False">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
566 <validator type="in_range" min="1"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
567 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
568 <param type="float" name="change" value="0.0005" label="Parameter change cutoff" optional="False" help="The cutoff for the absolute gradient values such that learning will cease if all values fall below this threshold.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
569 <validator type="in_range" min="0.00000001"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
570 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
571 <param type="float" name="step" value="0.5" label="Learning rate scaling factor" optional="False">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
572 <validator type="in_range" min="0.000001" max="1.0"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
573 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
574 <param type="select" name="precalc" label="Precalculate probability corrections from fragment means">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
575 <option value="-p">yes</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
576 <option value="">no</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
577 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
578 <param type="select" name="precalc" label="Precalculate probability corrections from fragment means">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
579 <option value="-p">yes</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
580 <option value="">no</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
581 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
582 <param type="integer" name="biniter" value="1000" label="Maximum number of binning iterations" optional="False">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
583 <validator type="in_range" min="1"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
584 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
585 <param type="float" name="threshold" value="1.0" label="Learning threshold" optional="False"
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
586 help="The minimum change needed in the log-likelihood to continue learning binning corrections.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
587 <validator type="in_range" min="0.000001" max="1.0"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
588 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
589 <param type="select" name="binreads" label="Reads to use for learning binning corrections.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
590 <option value="cis">cis</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
591 <option value="trans">trans</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
592 <option value="all">all</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
593 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
594 <param type="text" size="60" name="model" value="len" label="Model parameters" optional="False" help="A comma-separated list of fragment characteristics to learn corrections for. These can include 'len' and any characteristics included in the fragment bed file.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
595 <validator type="empty_field" />
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
596 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
597 <param type="text" size="60" name="modelbins" value="10" label="Number of parameter bins" optional="False" help="A comma-separated list of bins to divide each model parameter into.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
598 <validator type="empty_field" />
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
599 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
600 <param type="text" size="60" name="modeltypes" value="even" label="Parameter types" optional="False" help="A comma-separated list of model parameter types. These can be 'even', 'fixed', 'even-const', and 'fixed-const'.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
601 <validator type="empty_field" />
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
602 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
603 </when>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
604
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
605 <when value="express-binning">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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606 <param type="integer" name="expiter" value="1000" label="Number of express iterations" optional="False">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
607 <validator type="in_range" min="1"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
608 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
609 <param type="select" name="removedist" label="Remove estimated distance-dependence prior to learning express corrections.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
610 <option value="-d">yes</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
611 <option value="">no</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
612 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
613 <param type="select" name="expreads" label="Reads to use for learning express corrections.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
614 <option value="cis">cis</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
sauria
parents:
diff changeset
615 <option value="trans">trans</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
616 <option value="all">all</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
617 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
618 <param type="integer" name="biniter" value="1000" label="Maximum number of binning iterations" optional="False">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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parents:
diff changeset
619 <validator type="in_range" min="1"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
620 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
621 <param type="float" name="threshold" value="1.0" label="Learning threshold" optional="False"
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
622 help="The minimum change needed in the log-likelihood to continue learning binning corrections.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
623 <validator type="in_range" min="0.000001" max="1.0"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
624 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
625 <param type="select" name="binreads" label="Reads to use for learning binning corrections.">
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626 <option value="cis">cis</option>
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627 <option value="trans">trans</option>
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628 <option value="all">all</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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629 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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630 <param type="text" size="60" name="model" value="len" label="Model parameters" optional="False" help="A comma-separated list of fragment characteristics to learn corrections for. These can include 'len' and any characteristics included in the fragment bed file.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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631 <validator type="empty_field" />
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632 </param>
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633 <param type="text" size="60" name="modelbins" value="10" label="Number of parameter bins" optional="False" help="A comma-separated list of bins to divide each model parameter into.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
634 <validator type="empty_field" />
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635 </param>
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636 <param type="text" size="60" name="modeltypes" value="even" label="Parameter types" optional="False" help="A comma-separated list of model parameter types. These can be 'even', 'fixed', 'even-const', and 'fixed-const'.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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637 <validator type="empty_field" />
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638 </param>
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639 </when>
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640 </conditional>
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641 </xml>
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642 <token name="@5C_DATATYPE@">
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diff changeset
643 -d $command.datatype
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diff changeset
644 </token>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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645 <xml name="5c_datatype_xml">
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diff changeset
646 <!-- Options controlling type of 5c data to return -->
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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647 <param name="datatype" type="select" label="Datatype">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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648 <option value="raw">raw</option>
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649 <option value="fragment">fragment-corrected</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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650 <option value="distance">distance-corrected</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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651 <option value="enrichment">enrichment</option>
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652 </param>
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653 </xml>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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654 <token name="@BINSIZE@">
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655 -b $command.binsize
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656 </token>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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657 <xml name="binsize_xml">
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658 <!-- Options controlling binning size-->
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659 <param type="integer" name="binsize" value="10000" label="Binsize" optional="False" help="A value of zero will return unbinned data.">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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660 <validator type="in_range" min="0"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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661 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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662 </xml>
10
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663 <token name="@MRH_OPTIONS@">
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664 -f $command.mrhminobs
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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665 -b $command.mrhminbinsize
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666 -B $command.mrhmaxbinsize
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667 #if str( $command.mrhtransminbinsize ) != "":
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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668 -r $command.mrhtransminbinsize
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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669 #end if
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diff changeset
670 #if str( $command.mrhtransmaxbinsize ) != "":
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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671 -R $command.mrhtransmaxbinsize
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672 #end if
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673 </token>
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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674 <xml name="mrh_options_xml">
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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675 <param name="mrhminobs" type="integer" label="Minimum observations" value="20" help="The number of observations needed to include a bin." >
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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676 <validator type="in_range" min="1"/>
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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677 </param>
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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678 <!-- Options controlling binning sizes-->
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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679 <param type="integer" name="mrhminbinsize" label="Cis minimum binsize (bp)" value="5000" >
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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680 <validator type="in_range" min="1"/>
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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681 </param>
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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682 <param type="integer" name="mrhmaxbinsize" label="Cis maximum binsize (bp)" value="1280000" help="Must be a multiple of an integer power of two times the minimum binsize (i.e. minbin * 2^N = maxbin for an integer N). ">
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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diff changeset
683 <validator type="in_range" min="1"/>
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diff changeset
684 </param>
13
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685 <param type="integer" name="mrhtransminbinsize" label="Trans minimum binsize (bp)" value='' help="If not specified, this will be set to the cis minimum binsize." optional="True" />
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686 <param type="integer" name="mrhtransmaxbinsize" label="Trans maximum binsize (bp)" value='' help="If not specified, this will be set to the cis maximum binsize." optional="True" />
10
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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687 </xml>
9
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688 <token name="@HIC_DYNAMIC@">
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689 #if str( $command.dynamic.binning ) == "yes":
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690 -y
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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691 -x $command.dynamic.expbinsize
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692 -f $command.dynamic.minobs
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693 -a $command.dynamic.search
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694 $command.dynamic.failed
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695 #end if
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696 </token>
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697 <token name="@5C_DYNAMIC@">
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698 #if str( $command.dynamic.binning ) == "yes":
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699 -y
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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700 -x $command.dynamic.expbinsize
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diff changeset
701 -f $command.dynamic.minobs
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702 -g $command.dynamic.search
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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703 $command.dynamic.failed
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704 #end if
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705 </token>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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706 <xml name="dynamic_xml">
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707 <!-- Options controlling dynamic binning of data -->
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708 <conditional name="dynamic">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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709 <param name="binning" type="select" label="Dynamically bin data">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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710 <option value="no">no</option>
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711 <option value="yes">yes</option>
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712 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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713 <when value="yes">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
714 <param name="expbinsize" type="integer" label="Expansion binning size (bp)" value="10000" help="The size of bins to use when expanding heatmap bins. A zero indicates unbinned expansion." >
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diff changeset
715 <validator type="in_range" min="0"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
716 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
717 <param name="minobs" type="integer" label="Minimum observations" value="20" help="The number of observations needed to stop expanding a bin." >
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diff changeset
718 <validator type="in_range" min="1"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
719 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
720 <param name="search" type="integer" label="Maximum search distance" value="0" help="The maximum distance a bin can be expanded. A value of zero indicates no maximum." >
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
721 <validator type="in_range" min="0"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
722 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
723 <param name="failed" type="select" label="Remove failed bins">
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
724 <option value="">no</option>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
725 <option value="-v">yes</option>
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diff changeset
726 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
727 </when>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
728 <when value="no"/>
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diff changeset
729 </conditional>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
730 </xml>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
731 <token name="@IMAGE@">
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diff changeset
732 -k min_color=$command.image.mincolor
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diff changeset
733 -k mid_color=$command.image.midcolor
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diff changeset
734 -k max_color=$command.image.maxcolor
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diff changeset
735 -k logged=$command.image.logged
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736 #if $command.image.minscore:
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737 -k minscore=$command.image.minscore
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738 #end if
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
739 #if $command.image.maxscore:
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740 -k maxscore=$command.image.maxscore
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741 #end if
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742 </token>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
743 <xml name="image_xml">
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744 <!-- Options controlling hic image options -->
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745 <param name="mincolor" type="color" value="#0000ff" label="Minimum value color"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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746 <param name="midcolor" type="color" value="#ffffff" label="Middle value color"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
747 <param name="maxcolor" type="color" value="#ff0000" label="Maximum value color"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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748 <param name="logged" type="select" label="Logged values">
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749 <option value="true">yes</option>
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750 <option value="false">no</option>
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751 </param>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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752 <param name="minscore" type="float" optional="True" label="Minimum score limit"/>
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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diff changeset
753 <param name="maxscore" type="float" optional="True" label="Maximum score limit"/>
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diff changeset
754 </xml>
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755 <token name="@ROTATE@">
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diff changeset
756 $command.image.rotate
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757 </token>
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758 <xml name="rotate_xml">
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759 <!-- Options controlling hic image rotation -->
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760 <param name="rotate" type="select" label="Rotate image 45 degrees (horizontal axis)">
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761 <option value="">no</option>
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762 <option value="-r">yes</option>
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763 </param>
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diff changeset
764 </xml>
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765 <token name="@COMMAND_HELP@"><![CDATA[
5e3de32a8688 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
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766 HiFive is a tool for handling, normalizing, and plotting HiC and 5C chromatin interaction data. It has numerous normalization approaches built in with a variety of options, allowing for fine-scale control and data processing. HiFive is broken down into a series of selectable commands, each with a HiC or 5C version.
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diff changeset
767
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768 COMMANDS
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769 --------
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770
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771 Complete HiC analysis / Complete 5C analysis - this command creates a genome partion file, loads data into a dataset, creates a project file and performs data normalization on that project file.
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772
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773 Create HiC fend set / Create 5C fragment set - this command takes a bed file containing restriction fragment information and creates a HiFive partition file that will be used for downstream data processing.
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774
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775 Create HiC data set / Create 5C data set - this command loads data from BAM file pairs or a variety of other file formats, partitions reads according to the information in the HiFive genome partition file and creates a HiFive data file.
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776
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777 Create HiC project / Create 5C project - this command creates a HiFive project, associates a specific data set with it, constructs a distance-dependence function and filters fragments based on coverage.
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diff changeset
778
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779 Normalize HiC project / Normalize 5C project - this command provides a selection of normalization algorithms and finds correction values for data normalization.
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diff changeset
780
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781 Create HiC heatmap set / Create 5C heatmap set - this command creates a set of heatmaps, one per chromosome and, if selected, one per chromosome pair (trans), in a compact HDF5 format. Heatmaps can also be plotted at the time of creation.
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782
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783 Extract HiC interval / Extract 5C interval - this command returns a genomic interval files with data from a specified region. This data may also be plotted at the tie of extraction.
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784
10
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785 Create HiC multi-resolution heatmap - this command returns a multi-resolution heatmap file with data heatmapped across resolutions from the smallest to largest specified binsizes in 2X steps.
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786
9
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787 ]]></token>
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788 <token name="@HIC_HELP@"><![CDATA[
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789 HiC genomic partitioning - fend file
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790 ----------------------------------------
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791
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792 A bed file containing either restriction enzyme cutopoints or fragment bounds is converted into an hdf5-type fragment file of fragment characteristics. In addition to coordinates, strand, and chromosome information, additional columns can be included containing other fragment characteristics, such as GC content. If additional columns are included, they must be labeled in the header with a label containing no spaces or commas. These names can be used with the binning algorithm to include the fragment characteristic in the model to be learned. Additional characteristics should be comma-separated pairs of values corresponding to the upstream and downstream sides of the cutsite or ends of the fragment, depending on the whether the bed file contains cutsites or fragment coordinates, respectively.
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793
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794 HiC data
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795 --------
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796
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797 Reads are paired with the specified fend file, creating a HiFive dataset object. Data can be a series of paired-end bam files, a tabular format list of paired genomic positions (chromosome1 coordinate1 strand1 chromosome2 coordinate2 strand2), or a HiCPipe-style mat-formatted list of fend-pairs and observed read counts.
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798
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799 HiC project
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800 -----------
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801
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802 Fends are filtered in an iterative manner using the minimum interaction cutoff and interaction size parameters specified to ensure that all valid fends have at least the minimum number of interactions with other valid fends. Subsequently, a distance dependence approximation curve is calculated piecewise using the number of bins specified. The first bin encompasses all interactions less than or equal to the minimum bin cutoff value. The remaining bins are evenly sized between log(minimum cutoff) and log(max possible interaction size).
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803
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804 HiC normalization
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805 -----------------
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806
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807 Corrections values are learned for either each valid fend, ranges of fend characteristics, or both. The 'probability' and 'express' algorithms learn correction values associated with each fend while the 'binning' algorithm learns fend characteristic corrections. These can be chained together in either order to produce more robust corrections.
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808
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809 Using the probability algorithm, observation of counts are assumed to be distributed according to a binomial distribution with an observation probability for each interaction equal to the product of the distance-dependence signal and the two fend correction parameters. Using the probability algorithm, learning is done using a backtracking line gradient descent approach. Learning proceeds for up to the maximum number of iterations but is terminated early if all of the absolute gradient values fall below the cutoff threshold. At each step, the learning rate is scaled down by the step value if the current learning rate does not produce sufficient improvement as measured by the Arjimo criterion.
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810
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811 The express algorithm is a variant of matrix balancing and approximates the corrections through an iterative norm-2 adjustment to given all fragments a mean ratio of one for valid counts versus signal predicted from distance-dependence. This can be done using intra-regional interactions, inter-regional interactions, or all interactions.
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812
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813 The binning algorithm divides each model parameter into some number of bins and based on a binomial distribution, correction values for each bin are learned, maximizing the log-likelihood of the data. Model parameters can be the fend lengths ('len'), fend GC content ('gc'), and any other characteristics passed as additional columns (with header labels) in the bed file used to create the HiFive fend file. Each parameter has a number of bins specified to divide it into and can be partitioned according to its type to contain approximately equal numbers of fends ('even'), or to cover equal portions of the range of parameter values ('fixed'). In addition, parameter types can include the '-const' suffix to denote a parameter that should not be optimized after seeding.
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814
10
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815 HiC multi-resolution heatmapping
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816 --------------------------------
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817
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818 Multi-resolution heatmapping (MRH) allows multiple levels of resolution to be stored and accessed simultaneously using an intelligent binning scheme that only accepts bin with a number of observed reads meeting the minimum observation threshold. MRH files can be interactively explored through the MRH plugin in Galaxy.
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819
9
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820 ]]></token>
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821 <token name="@5C_HELP@"><![CDATA[
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822 5C genomic partitioning - fragment file
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823 ---------------------------------------
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824
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825 A bed file containing targeted restriction enzyme fragment boundaries is converted into an hdf5-type fragment file of fragment characteristics. In addition to coordinates, strand, and chromosome information, additional columns can be included containing other fragment characteristics, such as GC content. If additional columns are included, they must be labeled in the header with a label containing no spaces or commas. These names can be used with the binning algorithm to include the fragment characteristic in the model to be learned.
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826
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827 5C data
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828 -------
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829
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830 Reads are loaded and paired with the specified fragment file, creating a HiFive dataset object. Data can be a series of paired-end bam files or a tabular format list of paired fragments and their observed read count (fragment1 fragment2 count).
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831
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832 5C project
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833 ----------
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834
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835 Fragments are filtered in an iterative manner using the minimum interaction cutoff and interaction size parameters specified to ensure that all valid fragments have at least the minimum number of interactions with other valid fragments. Subsequently, a distance dependence approximation line is calculated using a regression line to approximate the linear relationship between log(# reads) and log(distance).
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836
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837 5C normalization
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838 ----------------
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839
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840 Corrections values are learned for either each valid fragment, ranges of fragment characteristics, or both. The 'probability' and 'express' algorithms learn correction values associated with each fragment while the 'binning' algorithm learns fragment characteristic corrections. These can be chained together in either order to produce more robust corrections.
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841
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842 The probability algorithm assumes non-zero counts to distributed according to a log-normal distribution with each interaction having a mean equal to the distance-depedence predicted signal times each of the interaction fragment correction parameters and a universal sigma value. Using the probability algorithm, learning is done using a backtracking line gradient descent approach. Learning proceeds for up to the maximum number of iterations but is terminated early if all of the absolute gradient values fall below the cutoff threshold. At each step, the learning rate is scaled down by the step value if the current learning rate does not produce sufficient improvement as measured by the Arjimo criterion.
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843
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844 The express algorithm is a variant of matrix balancing and approximates the corrections through an iterative norm-2 adjustment to given all fragments a mean ratio of one for valid counts versus predicted signal from distance-dependence. This can be done using intra-regional interactions, inter-regional interactions, or all interactions.
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845
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846 The binning algorithm divides each model parameter into some number of bins and based on a log-normal distribution, correction values for each bin are learned, maximizing the log-likelihood of the data. Model parameters can be the fragment lengths ('len') and any other characteristics passed as additional columns (with header labels) in the bed file used to create the HiFive fragment file. Each parameter has a number of bins specified to divide it into and can be partitioned according to its type to contain approximately equal numbers of fragments ('even'), or to cover equal portions of the range of parameter values ('fixed'). In addition, parameter types can include the '-const' suffix to denote a parameter that should not be optimized after seeding.
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847
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848 ]]></token>
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849 </macros>