Mercurial > repos > matthias > stacks2_procrad

annotate macros.xml @ 0:a4e62d5c5101 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
author matthias
date Thu, 29 Nov 2018 11:56:45 -0500
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children d2e1ef2f5575
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a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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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>
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5 <requirement type="package" version="@WRAPPER_VERSION@">stacks</requirement>
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6 <yield/>
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7 </requirements>
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8 </xml>
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9
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10 <token name="@WRAPPER_VERSION@">2.2=he860b03_0</token>
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11
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12 <xml name="stdio">
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13 <stdio>
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14 <exit_code range="1:" level="fatal" description="Error in Stacks execution" />
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15 </stdio>
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16 </xml>
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17
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18 <xml name="citation">
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19 <citations>
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20 <citation type="doi">10.1111/mec.12354</citation>
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21 <citation type="doi">10.1111/mec.12330</citation>
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22 <citation type="doi">10.1534/g3.111.000240</citation>
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23 <citation type="doi">10.1534/genetics.111.127324</citation>
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24 <citation type="doi">10.1111/j.1755-0998.2010.02967.x</citation>
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25 <citation type="doi">10.1073/pnas.1006538107</citation>
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26 </citations>
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27 </xml>
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28
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29 <xml name="version_cmd">
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30 <version_command><![CDATA[
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31 process_radtags -h |& grep process_radtags | head -n 1 | cut -d" " -f 2
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32 ]]>
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33 </version_command>
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34 </xml>
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35
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36 <token name="@STACKS_INFOS@">
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37 <![CDATA[
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38 --------
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39
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40 **Created by:**
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41
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42 Stacks was developed by Julian Catchen with contributions from Angel Amores, Paul Hohenlohe, and Bill Cresko
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43
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44 **Project links:**
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45
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46 `Stacks website <http://catchenlab.life.illinois.edu/stacks/>`_
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47
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48 `Stacks manual <http://catchenlab.life.illinois.edu/stacks/manual/>`_
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49
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50 `Stacks google group <http://groups.google.com/group/stacks-users>`_
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51 ]]></token>
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52
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53 <xml name="enzymes">
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54
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55 <option value="">Unspecified</option>
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56 <option value="aciI">aciI</option>
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57 <option value="ageI">ageI</option>
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58 <option value="aluI">aluI</option>
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59 <option value="apaLI">apaLI</option>
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60 <option value="apeKI">apeKI</option>
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61 <option value="apoI">apoI</option>
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62 <option value="aseI">aseI</option>
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63 <option value="bamHI">bamHI</option>
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64 <option value="bbvCI">bbvCI</option>
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65 <option value="bfaI">bfaI</option>
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66 <option value="bfuCI">bfuCI</option>
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67 <option value="bgIII">bgIII</option>
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68 <option value="bsaHI">bsaHI</option>
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69 <option value="bspDI">bspDI</option>
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70 <option value="bstYI">bstYI</option>
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71 <option value="cac8I">cac8I</option>
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72 <option value="claI">claI</option>
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73 <option value="csp6I">csp6I</option>
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74 <option value="ddeI">ddeI</option>
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75 <option value="dpnII">dpnII</option>
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76 <option value="eaeI">eaeI</option>
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77 <option value="ecoRI">ecoRI</option>
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78 <option value="ecoRV">ecoRV</option>
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79 <option value="ecoT22I">ecoT22I</option>
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80 <option value="haeIII">haeIII</option>
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81 <option value="hindIII">hindIII</option>
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82 <option value="hinP1I">hinP1I</option>
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83 <option value="hpaII">hpaII</option>
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84 <option value="kpnI">kpnI</option>
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85 <option value="mluCI">mluCI</option>
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86 <option value="mseI">mseI</option>
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87 <option value="mslI">mslI</option>
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88 <option value="mspI">mspI</option>
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89 <option value="ncoI">ncoI</option>
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90 <option value="ndeI">ndeI</option>
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91 <option value="nheI">nheI</option>
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92 <option value="nlaIII">nlaIII</option>
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93 <option value="notI">notI</option>
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94 <option value="nsiI">nsiI</option>
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95 <option value="nspI">nspI</option>
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96 <option value="pstI">pstI</option>
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97 <option value="rsaI">rsaI</option>
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98 <option value="sacI">sacI</option>
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99 <option value="sau3AI">sau3AI</option>
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100 <option value="sbfI">sbfI</option>
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101 <option value="sexAI">sexAI</option>
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102 <option value="sgrAI">sgrAI</option>
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103 <option value="speI">speI</option>
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104 <option value="sphI">sphI</option>
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105 <option value="taqI">taqI</option>
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106 <option value="xbaI">xbaI</option>
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107 <option value="xhoI">xhoI</option>
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108 </xml>
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109
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110 <!-- log file handling -->
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111 <token name="@TEE_APPEND_LOG@"><![CDATA[
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112 #if $output_log
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113 2>> $output_log &&
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114 #end if
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115 ]]></token>
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116 <token name="@CAT_LOG_TO_STDERR@"><![CDATA[
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117 #if $output_log
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118 cat $output_log 2>&1
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119 #end if
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120 ]]></token>
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121 <xml name="in_log">
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122 <param name="add_log" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Add log output as data set" />
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123 </xml>
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124 <xml name="out_log">
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125 <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file">
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126 <filter>add_log</filter>
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127 </data>
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128 </xml>
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129
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130 <!-- fastq input -->
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131 <xml name="fastq_input_macro" token_fastq_optional="false">
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132 <conditional name="input_type">
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133 <param name="input_type_selector" type="select" label="Short read data from individuals" help="Single end data or forward reads. If a paired list is provided only the forward reads are used in ustacks">
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134 <option value="manual" selected="true">single end or forward reads</option>
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135 <option value="list">(paired) data set list</option>
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136 </param>
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137 <when value="manual">
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138 <param name="samples" argument="-f" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" type="data" label="Reads" multiple="true" optional="@FASTQ_OPTIONAL@"/>
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139 </when>
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140 <when value="list">
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141 <param name="samples" argument="-f" type="data_collection" collection_type="list,list:paired" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="List for forward reads or read pairs" optional="@FASTQ_OPTIONAL@"/>
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142 </when>
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143 </conditional>
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144 </xml>
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145 <!-- requires a variable $read_direction=None|"forward"|"reverse" to be set
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146 appends noting/.1/.2 to the link name for accessing the fastq data
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147 sets variables $name and $data_path-->
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148 <token name="@FASTQ_INPUT@"><![CDATA[
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149 #set $name = $clean_ext($sample.name)
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150 #set $data_path = "stacks_inputs/" + $name
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151 #if $sample.is_collection:
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152 #set $sample=$sample[$read_direction]
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153 #end if
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154 #if $read_direction == "forward":
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155 #set $data_path = $data_path + ".1"
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156 #elif $read_direction == "reverse":
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157 #set $data_path = $data_path + ".2"
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158 #end if
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159 #if $sample.is_of_type('fastqsanger')
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160 #set $data_path = $data_path + ".fq"
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161 #set inputype = "fastq"
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162 #else if $sample.is_of_type('fastqsanger.gz')
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163 #set $data_path = $data_path + ".fq.gz"
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164 #set inputype = "gzfastq"
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165 #else if $sample.is_of_type('fasta')
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166 #set $data_path = $data_path + ".fa"
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167 #set inputype = "fasta"
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168 #else
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169 #set $data_path = $data_path + ".fa.gz"
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170 #set inputype = "gzfasta"
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171 #end if
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172 ln -s '$sample' '${data_path}' &&
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173 ]]></token>
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174
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175 <!-- macro and token for BAM input-->
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176 <xml name="bam_input_macro">
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177 <conditional name="input_type">
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178 <param name="input_type_selector" type="select" label="BAM files">
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179 <option value="list">data set list</option>
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180 <option value="manual">data sets</option>
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181 </param>
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182 <when value="manual">
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183 <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="BAM files" />
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184 </when>
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185 <when value="list">
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186 <param name="input_bam" format="bam" type="data_collection" collection_type="list" label="BAM files" />
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187 </when>
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188 </conditional>
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189 </xml>
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190 <token name="@BAM_INPUT@"><![CDATA[
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191 #set $bamlist = ""
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192 #for $bam in $input_type.input_bam:
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193 #set $filename = $clean_ext($bam.element_identifier)+".bam"
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194 #if re.search('.*\.bam$', $filename)
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195 ln -s '$bam' bam_inputs/$filename &&
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196 #set bamlist += " -B 'bam_inputs/"+$filename+"'"
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197 #end if
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198 #end for
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199 ]]></token>
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200
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201 <xml name="discover_faqgz_output_macro" token_pattern="" token_dir="">
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202 <expand macro="discover_faq_output_macro" pattern="@PATTERN@" dir="@DIR@"/>
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203 <discover_datasets pattern="@PATTERN@\.fq\.gz$" ext="fastqsanger.gz" directory="@DIR@/" />
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204 <discover_datasets pattern="@PATTERN@\.fa\.gz$" ext="fasta.gz" directory="@DIR@/" />
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205 </xml>
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206 <xml name="discover_faq_output_macro" token_pattern="" token_dir="">
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207 <discover_datasets pattern="@PATTERN@\.fq$" ext="fastqsanger" directory="@DIR@/" />
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208 <discover_datasets pattern="@PATTERN@\.fa$" ext="fasta" directory="@DIR@/" />
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209 </xml>
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210 <token name="@CLEAN_EXT@">
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211 <![CDATA[
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212 #from os.path import splitext
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213 #import re
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214 #def clean_ext($identifier)
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215 #while $identifier.endswith(('.1', '.2', '.fa', '.fq', '.fasta', '.fastq', '.gz', '.gzip', '.sam', '.bam'))
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216 #set $identifier = splitext($identifier)[0]
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217 #end while
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218 $identifier#slurp
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219 #end def
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220 ]]>
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221 </token>
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222
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223 <!-- tokens and macros for gapped alignment options
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224 the _onoff macro gives an empty conditional (which is not so nice
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225 but allows to be used also in the full macro) -->
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226 <token name="@GAP_OPTIONS@"><![CDATA[
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227 #if $gapped.use_gapped == "yes"
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228 --max_gaps $gapped.max_gaps
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229 --min_aln_len $gapped.min_aln_len
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230 #else
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231 --disable-gapped
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232 #end if
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233 ]]></token>
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234 <token name="@GAP_OPTIONS_ONOFF@"><![CDATA[
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235 #if $gapped.use_gapped != "yes"
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236 --disable-gapped
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237 #end if
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238 ]]></token>
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239 <xml name="gap_options">
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240 <expand macro="gap_options_onoff">
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241 <param argument="--max_gaps" type="float" value="2.0" label="Number of gaps allowed between stacks before merging"/>
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242 <param argument="--min_aln_len" type="float" value="0.8" min="0.0" max="1.0" label="Minimum length of aligned sequence in a gapped alignment"/>
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243 </expand>
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244 </xml>
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245 <xml name="gap_options_onoff">
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246 <conditional name="gapped">
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247 <param name="use_gapped" argument="--disable-gapped" type="select" label="Perform gapped alignments between stacks">
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248 <option value="no">No</option>
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249 <option value="yes" selected="true">Yes</option>
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250 </param>
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251 <when value="no"/>
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252 <when value="yes">
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253 <yield/>
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254 </when>
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255 </conditional>
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256 </xml>
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257
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258 <!-- ustacks outputs collection containing SAMPLE.tags.tsv, SAMPLE.snps.tsv, SAMPLE.alleles.tsv (SAMPLE!=catalog) -->
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259 <!-- TODO tags, snps, and alleles could go to sub collections -->
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260 <xml name="ustacks_outputs_macro" token_tooladd="">
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261 <collection name="tabs" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Stacks">
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262 <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
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263 <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
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264 <discover_datasets pattern="(?P&lt;name&gt;(?!catalog).+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
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265 </collection>
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266 </xml>
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267 <!-- cstacks outputs collection containing catalog.tags.tsv, catalog.snps.tsv, catalog.alleles.tsv -->
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268 <xml name="cstacks_outputs_macro" token_tooladd="">
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269 <collection name="catalog" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Catalog">
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270 <discover_datasets pattern="(?P&lt;name&gt;catalog\.(tags|snps|alleles))\.tsv$" ext="tabular" directory="stacks_outputs" />
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271 </collection>
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272 </xml>
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273 <!-- sstacks outputs collection containing SAMPLE.matches.tsv -->
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274 <xml name="sstacks_outputs_macro" token_tooladd="">
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275 <collection name="matches" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Matches to the catalog">
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276 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" />
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277 </collection>
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278 </xml>
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279 <!-- tsv2bam outputs collection containing SAMPLE.matches.bam -->
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280 <xml name="tsv2bam_outputs_macro" token_tooladd="">
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281 <collection name="bams" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Stacks">
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282 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.bam$" ext="bam" directory="stacks_outputs" />
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283 </collection>
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284 </xml>
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285 <!-- gstacks outputs collection containing catalog.calls.vcf and catalog.fa.gz -->
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286 <xml name="gstacks_outputs_macro" token_tooladd="">
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287 <collection name="gstacks_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string}">
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288 <discover_datasets pattern="(?P&lt;name&gt;catalog\.calls\.vcf)$" ext="vcf" directory="stacks_outputs" />
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289 <discover_datasets pattern="(?P&lt;name&gt;catalog\.fa\.gz)$" ext="fasta.gz" directory="stacks_outputs" />
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290 </collection>
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291 </xml>
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292
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293 <!-- default output of populations -->
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294 <xml name="populations_output_light" token_tooladd="">
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295 <data format="tabular" name="out_haplotypes" label="${tool.name} @TOOLADD@ on ${on_string} Raw Genotypes/Haplotypes" from_work_dir="stacks_outputs/populations.haplotypes.tsv" />
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296 <data format="tabular" name="out_hapstats" label="${tool.name} @TOOLADD@ on ${on_string} Population-level haplotype summary statistics" from_work_dir="stacks_outputs/populations.hapstats.tsv" />
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297 <data format="txt" name="out_populations_log_distribs" label="${tool.name} @TOOLADD@ on ${on_string} Populations log distributions" from_work_dir="stacks_outputs/populations.log.distribs" />
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298 <data format="tabular" name="out_sumstats_sum" label="${tool.name} @TOOLADD@ on ${on_string} Summary of Population-level summary statistics" from_work_dir="stacks_outputs/populations.sumstats_summary.tsv" />
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299 <data format="tabular" name="out_sumstats" label="${tool.name} @TOOLADD@ on ${on_string} Population-level summary statistics" from_work_dir="stacks_outputs/populations.sumstats.tsv" />
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300 <data format="tabular" name="out_sql" label="${tool.name} @TOOLADD@ on ${on_string} Genotyping markers" from_work_dir="stacks_outputs/populations.markers.tsv" />
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301 </xml>
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302
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303 <xml name="populations_output_full">
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304 <expand macro="populations_output_light"/>
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305
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306 <!-- log_fst_comp populations.fst_summary.tsv populations.phistats_summary.tsv populations.phistats.tsv-->
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307 <data format="tabular" name="out_phistats" label="${tool.name} on ${on_string} Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats.tsv">
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308 <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter>
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309 </data>
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310 <data format="tabular" name="out_phistats_sum" label="${tool.name} on ${on_string} Summary of Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats_summary.tsv">
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311 <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter>
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312 </data>
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313 <data format="tabular" name="out_fststats_sum" label="${tool.name} on ${on_string} Summary of Fst statistics" from_work_dir="stacks_outputs/populations.fst_summary.tsv">
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314 <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter>
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315 </data>
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316
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317 <!-- fasta_loci populations.loci.fa
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318 fasta_samples populations.samples.fa
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319 fasta_samples_raw populations.samples-raw.fa-->
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320 <data format="tabular" name="out_fasta_strict" label="${tool.name} on ${on_string} per-locus consensus sequences" from_work_dir="stacks_outputs/populations.loci.fa">
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321 <filter>populations_output['fasta_loci']</filter>
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322 </data>
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323 <data format="tabular" name="out_fasta" label="${tool.name} on ${on_string} per-locus, per-haplotpye sequences" from_work_dir="stacks_outputs/populations.samples.fa">
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324 <filter>populations_output['fasta_samples']</filter>
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325 </data>
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326 <data format="tabular" name="out_fasta_raw" label="${tool.name} on ${on_string} per-locus, per-haplotpye sequences (regardless of biological plausibility)" from_work_dir="stacks_outputs/populations.samples-raw.fa">
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327 <filter>populations_output['fasta_samples_raw']</filter>
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328 </data>
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329
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330 <!-- phylip populations.fixed.phylip populations.fixed.phylip.log
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331 phylip_var populations.var.phylip populations.var.phylip.log-->
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332 <data format="tabular" name="out_phylip_all_pop_fix" label="${tool.name} on ${on_string} Phylip nucleotides that are fixed-within, and variant among populations" from_work_dir="stacks_outputs/populations.fixed.phylip">
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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333 <filter>populations_output['phylip']</filter>
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334 </data>
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335 <data format="tabular" name="out_phylip_all_loci_fix" label="${tool.name} on ${on_string} Phylip (loci) nucleotides that are fixed-within, and variant among populations" from_work_dir="stacks_outputs/populations.fixed.phylip.log">
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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336 <filter>populations_output['phylip']</filter>
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337 </data>
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338 <data format="tabular" name="out_phylip_all_pop_var" label="${tool.name} on ${on_string} Phylip all sequence as well as variable sites" from_work_dir="stacks_outputs/populations.var.phylip">
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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339 <filter>populations_output['phylip_var']</filter>
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340 </data>
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341 <data format="tabular" name="out_phylip_all_loci_var" label="${tool.name} on ${on_string} Phylip (loci) all sequence as well as variable sites" from_work_dir="stacks_outputs/populations.var.phylip.log">
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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342 <filter>populations_output['phylip_var']</filter>
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343 </data>
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344
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345 <!-- genepop populations.haps.genepop populations.snps.genepop -->
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346 <data format="tabular" name="out_genepop_snps" label="${tool.name} on ${on_string} SNPs in GenePop format" from_work_dir="stacks_outputs/populations.snps.genepop">
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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347 <filter>populations_output['genepop']</filter>
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348 </data>
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349 <data format="tabular" name="out_genepop_haps" label="${tool.name} on ${on_string} Haplotypes in GenePop format" from_work_dir="stacks_outputs/populations.haps.genepop">
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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350 <filter>populations_output['genepop']</filter>
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351 </data>
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352
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353 <!-- vcf populations.haps.vcf populations.snps.vcf -->
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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354 <data format="vcf" name="out_vcf_haplotypes_snps" label="${tool.name} on ${on_string} SNPs in VCF format" from_work_dir="stacks_outputs/populations.snps.vcf">
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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355 <filter>populations_output['vcf']</filter>
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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356 </data>
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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357 <data format="vcf" name="out_vcf_haplotypes_haps" label="${tool.name} on ${on_string} Haplotypes in VCF format" from_work_dir="stacks_outputs/populations.haps.vcf">
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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358 <filter>populations_output['vcf']</filter>
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359 </data>
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360
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361 <!--plink populations.plink.map populations.plink.ped-->
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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362 <data format="tabular" name="out_plink_markers" label="${tool.name} on ${on_string} PLINK (makers)" from_work_dir="stacks_outputs/populations.plink.map">
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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363 <filter>populations_output['plink']</filter>
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364 </data>
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365 <data format="tabular" name="out_plink_genotypes" label="${tool.name} on ${on_string} PLINK format (genotypes)" from_work_dir="stacks_outputs/populations.plink.ped">
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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366 <filter>populations_output['plink']</filter>
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367 </data>
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368
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369 <!--structure populations.structure-->
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370 <data format="tabular" name="out_structure" label="${tool.name} on ${on_string} Structure format" from_work_dir="stacks_outputs/populations.structure">
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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371 <filter>populations_output['structure']</filter>
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372 </data>
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373
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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374 <!-- radpainter populations.haps.radpainter -->
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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375 <data format="tabular" name="out_radpainter" label="${tool.name} on ${on_string} Radpainter format" from_work_dir="stacks_outputs/populations.haps.radpainter">
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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376 <filter>populations_output['radpainter']</filter>
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377 </data>
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378
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379 </xml>
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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380
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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381 <xml name="snp_options_alpha">
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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382 <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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383 <option value="0.1">0.1</option>
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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384 <option value="0.05" selected="True">0.05</option>
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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385 <option value="0.01">0.01</option>
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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386 <option value="0.001">0.001</option>
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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387 </param>
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388 </xml>
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389
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390 <xml name="snp_options">
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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391 <conditional name="select_model">
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392 <param argument="--model_type" type="select" label="Choose the model">
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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393 <option value="snp" selected="true">SNP</option>
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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394 <option value="bounded">Bounded SNP</option>
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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395 <option value="fixed">Fixed</option>
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396 </param>
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397 <when value="snp">
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398 <expand macro="snp_options_alpha"/>
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399 </when>
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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400 <when value="bounded">
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401 <param argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/>
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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402 <param argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" />
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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403 <expand macro="snp_options_alpha"/>
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404 </when>
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405 <when value="fixed">
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406 <yield/>
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407 </when>
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408 </conditional>
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409 </xml>
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410 <xml name="snp_options_full">
a4e62d5c5101 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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411 <expand macro="snp_options">
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412 <param argument="--bc_err_freq" type="float" value="0.1" min="0.0" max="1.0" label="Barcode error frequency" help="between 0 and 1.0"/>
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413 </expand>
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414 </xml>
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415
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416 <!-- variant calling option for use in gstacks and denovomap -->
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417 <xml name="variant_calling_options_vg">
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418 <param argument="--var-alpha" name="var_alpha" type="float" value="0.05" min="0" label="alpha threshold for discovering SNPs" />
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419 <expand macro="variant_calling_options_g"/>
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420 </xml>
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421 <xml name="variant_calling_options_g">
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422 <param argument="--gt-alpha" name="gt_alpha" type="float" value="0.05" min="0" label="alpha threshold for calling genotypes" />
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423 </xml>
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424
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425 <xml name="barcode_encoding_single">
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426 <option value="--inline_null" selected="True">Barcode is inline with sequence, occurs only on single-end read</option>
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427 <option value="--index_null">Barcode is provded in FASTQ header (Illumina i5 or i7 read)</option>
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428 <yield/>
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429 </xml>
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430
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431 <xml name="barcode_encoding_pair">
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432 <expand macro="barcode_encoding_single">
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433 <option value="--null_index">barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided)</option>
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434 <option value="--inline_inline">barcode is inline with sequence, occurs on single and paired-end read</option>
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435 <option value="--index_index">barcode is provded in FASTQ header (Illumina i5 and i7 reads).</option>
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436 <option value="--inline_index">barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read)</option>
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437 <option value="--index_inline"></option>
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438 </expand>
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439 </xml>
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440 </macros>