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annotate bowtie2_macros.xml @ 17:69f044db2445 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
author iuc
date Tue, 14 Nov 2017 15:02:02 -0500
parents 7e0b333f39e1
children 5e52e98ff239
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7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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1 <macros>
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2 <!-- Import this at the top of your command block and then
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3 define rg_auto_name. -->
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4 <token name="@define_read_group_helpers@">
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5 #def identifier_or_name($input1)
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6 #if hasattr($input1, 'element_identifier')
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7 #return $input1.element_identifier
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8 #else
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9 #return $input1.name.rstrip('.gz').rstrip('.fastq').rstrip('.fq').rstrip('.bz2')
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10 #end if
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11 #end def
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13 #def clean(name)
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14 #import re
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15 #set $name_clean = re.sub('[^\w\-_\.]', '_', $name)
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16 #return $name_clean
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17 #end def
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19 #def read_group_name_default($input1, $input2=None)
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20 #if $input2 is None
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21 #return $clean($identifier_or_name($input1))
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22 #else
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23 #import itertools
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24 #set $input_name1 = $clean($identifier_or_name($input1))
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25 #set $input_name2 = $clean($identifier_or_name($input2))
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26 #set $common_prefix = ''.join([c[0] for c in itertools.takewhile(lambda x: all(x[0] == y for y in x), itertools.izip(*[$input_name1, $input_name2]))])
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27 #if len($common_prefix) > 3
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28 #return $common_prefix
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29 #else
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30 #return $input_name1
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31 #end if
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32 #end if
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33 #end def
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35 #def format_read_group(prefix, value, quote='', arg='')
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36 #if $value
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37 #return $arg + $quote + $prefix + $value + $quote
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38 #else
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39 #return ''
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40 #end if
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41 #end def
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43 #def rg_param(name)
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44 #if $varExists("rg")
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45 #return $rg.get($name, None)
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46 #else
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47 #return $getVar($name, None)
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48 #end if
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49 #end def
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50
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51 #set $use_rg = True
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52 </token>
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53 <!-- preconditions use_rg and rg_auto_name have been
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54 defined.
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55 -->
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56 <token name="@set_read_group_vars@">
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57 #if $use_rg
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58 #if $rg_param('read_group_id_conditional') is None
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59 #set $rg_id = $rg_auto_name
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60 #elif $rg_param('read_group_id_conditional').do_auto_name
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61 #set $rg_id = $rg_auto_name
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62 #else
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63 #set $rg_id = str($rg_param('read_group_id_conditional').ID)
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64 #end if
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65
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66 #if $rg_param('read_group_sm_conditional') is None
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67 #set $rg_sm = ''
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68 #elif $rg_param('read_group_sm_conditional').do_auto_name
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69 #set $rg_sm = $rg_auto_name
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70 #else
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71 #set $rg_sm = str($rg_param('read_group_sm_conditional').SM)
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72 #end if
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73
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74 #if $rg_param('PL')
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75 #set $rg_pl = str($rg_param('PL'))
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76 #else
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77 #set $rg_pl = ''
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78 #end if
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79
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80 #if $rg_param('read_group_lb_conditional') is None
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81 #set $rg_lb = ''
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82 #elif $rg_param('read_group_lb_conditional').do_auto_name
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83 #set $rg_lb = $rg_auto_name
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84 #else
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85 #set $rg_lb = str($rg_param('read_group_lb_conditional').LB)
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86 #end if
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87
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88 #if $rg_param('CN')
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89 #set $rg_cn = str($rg_param('CN'))
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90 #else
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91 #set $rg_cn = ''
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92 #end if
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93
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94 #if $rg_param("DS")
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95 #set $rg_ds = str($rg_param("DS"))
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96 #else
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97 #set $rg_ds = ''
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98 #end if
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99
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100 #if $rg_param("DT")
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101 #set $rg_dt = str($rg_param("DT"))
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102 #else
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103 #set $rg_dt = ''
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104 #end if
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105
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106 #if $rg_param("FO")
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107 #set $rg_fo = str($rg_param("FO"))
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108 #else
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109 #set $rg_fo = ''
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110 #end if
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111
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112 #if $rg_param("KS")
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113 #set $rg_ks = str($rg_param("KS"))
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114 #else
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115 #set $rg_ks = ''
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116 #end if
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117
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118 #if $rg_param("PG")
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119 #set $rg_pg = str($rg_param("PG"))
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120 #else
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121 #set $rg_pg = ''
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122 #end if
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123
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124 #if $rg_param("PI") != None
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125 #set $rg_pi = str($rg_param("PI"))
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126 #else
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127 #set $rg_pi = ''
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128 #end if
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129
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130 #if $rg_param("PU")
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131 #set $rg_pu = str($rg_param("PU"))
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132 #else
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133 #set $rg_pu = ''
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134 #end if
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135 #end if
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136 </token>
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137 <token name="@set_use_rg_var@">
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138 #set $use_rg = str($rg.rg_selector) != "do_not_set"
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139 </token>
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140 <xml name="read_group_auto_name_conditional">
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141 <param name="do_auto_name" type="boolean" label="Auto-assign" help="Use dataset name or collection information to automatically assign this value" checked="false" />
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142 <when value="true">
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143 </when>
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144 <when value="false">
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145 <yield />
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146 </when>
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147 </xml>
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148 <xml name="read_group_id_param">
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149 <param name="ID" type="text" value="" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment" optional="false">
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150 <validator type="empty_field" />
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151 </param>
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152 </xml>
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153 <xml name="read_group_id_conditional">
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154 <conditional name="read_group_id_conditional">
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155 <expand macro="read_group_auto_name_conditional">
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156 <expand macro="read_group_id_param" />
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157 </expand>
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158 </conditional>
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159 </xml>
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160 <xml name="read_group_sm_param">
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161 <param name="SM" type="text" value="" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced" />
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162 </xml>
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163 <xml name="read_group_sm_conditional">
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164 <conditional name="read_group_sm_conditional">
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165 <expand macro="read_group_auto_name_conditional">
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166 <expand macro="read_group_sm_param" />
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167 </expand>
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168 </conditional>
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169 </xml>
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170 <!-- Above SM param is optional (for SAM/BAM spec, this is required
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171 as per Picard.
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172 -->
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173 <xml name="read_group_sm_param_required">
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174 <param name="SM" type="text" value="" label="Read group sample name (SM)" optional="false" help="This value should be descriptive. Use pool name where a pool is being sequenced">
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175 <validator type="empty_field" />
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176 </param>
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177 </xml>
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178 <xml name="read_group_sm_required_conditional">
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179 <conditional name="read_group_sm_conditional">
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180 <expand macro="read_group_auto_name_conditional">
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181 <expand macro="read_group_sm_param" />
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182 </expand>
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183 </conditional>
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184 </xml>
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185 <xml name="read_group_pl_param">
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186 <param name="PL" type="select" label="Platform/technology used to produce the reads (PL)">
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187 <option value="CAPILLARY">CAPILLARY</option>
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188 <option value="LS454">LS454</option>
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189 <option selected="True" value="ILLUMINA">ILLUMINA</option>
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190 <option value="SOLID">SOLID</option>
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191 <option value="HELICOS">HELICOS</option>
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192 <option value="IONTORRENT">IONTORRENT</option>
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193 <option value="PACBIO">PACBIO</option>
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194 </param>
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195 </xml>
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196 <xml name="read_group_lb_param">
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197 <param name="LB" type="text" label="Library name (LB)" optional="true" />
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198 </xml>
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199 <xml name="read_group_lb_conditional">
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200 <conditional name="read_group_lb_conditional">
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201 <expand macro="read_group_auto_name_conditional">
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202 <expand macro="read_group_lb_param" />
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203 </expand>
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204 </conditional>
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205 </xml>
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206 <xml name="read_group_lb_required_param">
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207 <param name="LB" type="text" label="Library name (LB)" optional="false">
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208 <validator type="empty_field" />
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209 </param>
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210 </xml>
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211 <xml name="read_group_lb_required_conditional">
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212 <conditional name="read_group_lb_conditional">
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213 <expand macro="read_group_auto_name_conditional">
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214 <expand macro="read_group_lb_required_param" />
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215 </expand>
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216 </conditional>
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217 </xml>
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218 <xml name="read_group_cn_param">
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219 <param name="CN" type="text" label="Sequencing center that produced the read (CN)" />
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220 </xml>
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221 <xml name="read_group_ds_param">
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222 <param name="DS" type="text" label="Description (DS)" />
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223 </xml>
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224 <xml name="read_group_dt_param">
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225 <param name="DT" type="text" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" />
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226 </xml>
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227 <xml name="read_group_fo_param">
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228 <param name="FO" type="text" optional="true" label="Flow order (FO)" help="The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\*|[ACMGRSVTWYHKDBN]+/">
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229 <validator type="regex" message="Invalid flow order">\*|[ACMGRSVTWYHKDBN]+$</validator>
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230 </param>
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231 </xml>
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232 <xml name="read_group_ks_param">
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233 <param name="KS" type="text" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" />
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234 </xml>
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235 <xml name="read_group_pg_param">
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236 <param name="PG" type="text" label="Programs used for processing the read group (PG)" />
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237 </xml>
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238 <xml name="read_group_pi_param">
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239 <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" />
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240 </xml>
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241 <xml name="read_group_pu_param">
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242 <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" />
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243 </xml>
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244 <xml name="read_group_pu_required_param">
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245 <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" />
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246 </xml>
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247 <!-- Only ID is required - all groups available -->
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248 <xml name="read_group_inputs_spec">
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249 <expand macro="read_group_id_conditional" />
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250 <expand macro="read_group_sm_conditional" />
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251 <expand macro="read_group_pl_param" />
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252 <expand macro="read_group_lb_conditional" />
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253 <expand macro="read_group_cn_param" />
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254 <expand macro="read_group_ds_param" />
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255 <expand macro="read_group_dt_param" />
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256 <expand macro="read_group_fo_param" />
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257 <expand macro="read_group_ks_param" />
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258 <expand macro="read_group_pg_param" />
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259 <expand macro="read_group_pi_param" />
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260 <expand macro="read_group_pu_param" />
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261 </xml>
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262 <!-- ID, SM, LB, PU, PL all required - not ks, pg, or fo params. -->
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263 <xml name="read_group_inputs_picard">
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264 <expand macro="read_group_id_conditional" />
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265 <expand macro="read_group_sm_required_conditional" />
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266 <expand macro="read_group_lb_required_conditional" />
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267 <expand macro="read_group_pl_param" />
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268 <expand macro="read_group_pu_required_param" />
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269 <expand macro="read_group_cn_param" />
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270 <expand macro="read_group_ds_param" />
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271 <expand macro="read_group_pi_param" />
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272 <expand macro="read_group_dt_param" />
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273 </xml>
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274 <xml name="read_group_conditional">
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275 <conditional name="rg">
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276 <param name="rg_selector" type="select" label="Set read groups information?" help="Specifying read group information can greatly simplify your downstream analyses by allowing combining multiple datasets.">
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277 <option value="set">Set read groups (SAM/BAM specification)</option>
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278 <option value="set_picard">Set read groups (Picard style)</option>
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279 <option value="set_id_auto">Automatically assign ID using name of history item(s)</option>
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280 <option value="do_not_set" selected="True">Do not set</option>
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281 </param>
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282 <when value="set_picard">
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283 <expand macro="read_group_inputs_picard" />
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284 </when>
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285 <when value="set">
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286 <expand macro="read_group_inputs_spec" />
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287 </when>
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288 <when value="set_id_auto">
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289 </when>
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290 <when value="do_not_set">
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291 </when>
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292 </conditional>
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293 </xml>
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294 <xml name="paired_end_options">
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295 <conditional name="paired_options">
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296 <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information">
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297 <option value="no" selected="True">No</option>
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298 <option value="yes">Yes</option>
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299 </param>
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300 <when value="yes">
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301 <param argument="-I" type="integer" value="0" min="0" label="Set the minimum fragment length for valid paired-end alignments"
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302 help="E.g. if `-I 60` is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as `-X` is also satisfied). A 19-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the `-I` constraint is applied with respect to the untrimmed mates. The larger the difference between `-I` and `-X`, the slower Bowtie 2 will run. This is because larger differences bewteen `-I` and `-X` require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient. Default=0"/>
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303 <param argument="-X" type="integer" value="500" min="0" label="Set the maximum fragment length for valid paired-end alignments"
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304 help="E.g. if `-X 100` is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the `-X` constraint is applied with respect to the untrimmed mates, not the trimmed mates; Default=500"/>
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305 <param name="fr_rf_ff" type="select" display="radio" label="Select the upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand"
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306 help="--fr, --rf, or --ff; E.g., if `--fr` is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length constraints (`-I` and `-X`) are met, that alignment is valid. Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid. `--rf` likewise requires that an upstream mate1 be reverse-complemented and a downstream mate2 be forward-oriented. `--ff` requires both an upstream mate 1 and a downstream mate 2 to be forward-oriented; Default=--fr (appropriate for Illumina's Paired-end Sequencing Assay)">
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307 <option value="--fr" selected="True">--fr</option>
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308 <option value="--rf">--rf</option>
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309 <option value="--ff">--ff</option>
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310 </param>
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311 <param argument="--no-mixed" name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/>
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312 <param argument="--no-discordant" name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/>
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313 <param argument="--dovetail" name="dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/>
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314 <param argument="--no-contain" name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Disallow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/>
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315 <param argument="--no-overlap" name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Disallow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/>
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316 </when>
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317 <when value="no">
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318 <!-- do nothing -->
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319 </when>
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320 </conditional>
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321 </xml>
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322 <xml name="align_unalign">
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323 <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc (possibly with -gz or -bz2); This triggers --un parameter for single reads and --un-conc for paired reads" />
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324 <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" help="--al/--al-conc (possibly with -gz or -bz2); This triggers --al parameter for single reads and --al-conc for paired reads" />
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325 </xml>
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326 </macros>