annotate macros.xml @ 23:c4b82dce8335 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
author iuc
date Fri, 30 Apr 2021 10:13:37 +0000
parents 093678460093
children 288f97432497
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1 <macros>
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2
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3 <token name="@read1_options@"><![CDATA[
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4
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5 ## Read1 trimming
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6
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7 #for $a in $library.r1.adapters
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8 #if $a.adapter_source.adapter_source_list == 'builtin':
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9 -a '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}'
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10 #else if $a.adapter_source.adapter_source_list == 'file':
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11 -a file:'${a.adapter_source.adapter_file}'
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12 #else if str($a.adapter_source.adapter_name) != "":
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13 -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}'
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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14 #else
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15 -a '${a.adapter_source.adapter}'
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16 #end if
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17 #end for
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18 #for $aa in $library.r1.anywhere_adapters
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19 #if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'builtin':
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20 -b '${aa.anywhere_adapter_source.anywhere_adapter.fields.name}'='${aa.anywhere_adapter_source.anywhere_adapter}'
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21 #else if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'file':
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22 -b file:'${aa.anywhere_adapter_source.anywhere_adapter_file}'
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23 #else if str($aa.anywhere_adapter_source.anywhere_adapter_name) != "":
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24 -b '${aa.anywhere_adapter_source.anywhere_adapter_name}'='${aa.anywhere_adapter_source.anywhere_adapter}'
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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25 #else
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26 -b '${aa.anywhere_adapter_source.anywhere_adapter}'
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27 #end if
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28 #end for
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29 #for $fa in $library.r1.front_adapters
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30 #if $fa.front_adapter_source.front_adapter_source_list == 'builtin':
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31 -g '${fa.front_adapter_source.front_adapter.fields.name}'='${fa.front_adapter_source.front_adapter}'
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32 #else if $fa.front_adapter_source.front_adapter_source_list == 'file':
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33 -g file:'${fa.front_adapter_source.front_adapter_file}'
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34 #else if str($fa.front_adapter_source.front_adapter_name) != "":
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35 -g '${fa.front_adapter_source.front_adapter_name}'='${fa.front_adapter_source.front_adapter}'
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36 #else
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37 -g '${fa.front_adapter_source.front_adapter}'
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38 #end if
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39 #end for
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40
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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41 #if str($library.r1.cut) != '0':
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42 -u $library.r1.cut
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43 #end if
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44
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45 ## Additional Outputs
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46
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47 #if $output_options.info_file:
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48 --info-file=$info_file
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49 #end if
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50 #if $output_options.rest_file:
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51 --rest-file='${rest_output}'
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52 #end if
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53 #if $output_options.wildcard_file:
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54 --wildcard-file='${wild_output}'
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55 #end if
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56 #if $output_options.too_short_file:
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57 --too-short-output='${too_short_output}'
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58 #end if
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59 #if $output_options.too_long_file:
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60 --too-long-output='${too_long_output}'
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61 #end if
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62 #if $output_options.untrimmed_file:
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63 --untrimmed-output='${untrimmed_output}'
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64 #end if
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65
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66 ]]></token>
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67
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68 <token name="@read2_options@"><![CDATA[
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69
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70 ## Read2 trimming
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71
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72 #for $a in $library.r2.adapters2
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73 #if $a.adapter_source2.adapter_source_list2 == 'builtin':
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74 -A '${a.adapter_source2.adapter2.fields.name}'='${a.adapter_source2.adapter2}'
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75 #else if $a.adapter_source2.adapter_source_list2 == 'file':
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76 -A file:'${a.adapter_source2.adapter_file2}'
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77 #else if str($a.adapter_source2.adapter_name2) != "":
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78 -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}'
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79 #else
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80 -A '${a.adapter_source2.adapter2}'
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81 #end if
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82 #end for
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83 #for $aa in $library.r2.anywhere_adapters2
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84 #if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'builtin':
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85 -B '${aa.anywhere_adapter_source2.anywhere_adapter2.fields.name}'='${aa.anywhere_adapter_source2.anywhere_adapter2}'
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86 #else if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'file':
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87 -B file:'${aa.anywhere_adapter_source2.anywhere_adapter_file2}'
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88 #else if str($aa.anywhere_adapter_source2.anywhere_adapter_name2) != "":
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89 -B '${aa.anywhere_adapter_source2.anywhere_adapter_name2}'='${aa.anywhere_adapter_source2.anywhere_adapter2}'
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90 #else
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91 -B '${aa.anywhere_adapter_source2.anywhere_adapter2}'
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92 #end if
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93 #end for
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94 #for $fa in $library.r2.front_adapters2
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95 #if $fa.front_adapter_source2.front_adapter_source_list2 == 'builtin':
22
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96 -G '${fa.front_adapter_source2.front_adapter2.fields.name}'='${fa.front_adapter_source2.front_adapter2}'
19
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97 #else if $fa.front_adapter_source2.front_adapter_source_list2 == 'file':
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98 -G file:'${fa.front_adapter_source2.front_adapter_file2}'
11
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99 #else if str($fa.front_adapter_source2.front_adapter_name2) != "":
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100 -G '${fa.front_adapter_source2.front_adapter_name2}'='${fa.front_adapter_source2.front_adapter2}'
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101 #else
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102 -G '${fa.front_adapter_source2.front_adapter2}'
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103 #end if
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104 #end for
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105
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106 #if str($library.r2.cut2) != '0':
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107 -U $library.r2.cut2
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108 #end if
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109
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110 ## Additional Outputs - Read 2
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111
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112 #if $output_options.too_short_file:
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113 --too-short-paired-output='${too_short_paired_output}'
11
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114 #end if
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115 #if $output_options.too_long_file:
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116 --too-long-paired-output='${too_long_paired_output}'
11
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117 #end if
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118 #if $output_options.untrimmed_file:
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119 --untrimmed-paired-output='${untrimmed_paired_output}'
11
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120 #end if
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121
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122 ]]></token>
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123
22
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124 <xml name="adapter_sanitizer">
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125 <sanitizer>
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126 <valid initial="string.digits">
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127 <add value="A"/><!--standard nucleotides-->
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128 <add value="T"/>
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129 <add value="C"/>
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130 <add value="G"/>
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131
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132 <add value="U"/><!--ambiguous nucleotides-->
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133 <add value="R"/>
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134 <add value="Y"/>
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135 <add value="S"/>
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136 <add value="W"/>
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137 <add value="K"/>
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138 <add value="M"/>
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139 <add value="B"/>
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140 <add value="D"/>
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141 <add value="H"/>
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142 <add value="V"/>
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143 <add value="N"/>
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144
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
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145 <add value="X"/><!-- don't match any nucleotide-->
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146
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
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147 <add value="{"/><!--specify repeats .. needs digits which are added as default-->
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148 <add value="}"/>
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149
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
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150 <add value="^"/><!--anchoring-->
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151 <add value="$"/>
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152 <add value="."/>
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153 <add value="("/><!--specify what to keep-->
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154 <add value=")"/>
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155
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
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156 </valid>
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157 </sanitizer>
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158 </xml>
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159
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
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160 <xml name="adapter" token_name="" token_argument="" token_value="" token_label="">
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161 <param name="@NAME@" argument="@ARGUMENT@" type="text" value="@VALUE@" label="@LABEL@">
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
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162 <expand macro="adapter_sanitizer"/>
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163 </param>
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164 </xml>
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165
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
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166 <xml name="adapter_select" token_name="" token_argument="" token_label="">
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167 <param name="@NAME@" argument="@ARGUMENT@" type="select" label="@LABEL@">
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168 <options from_data_table="adapters">
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169 <filter type="sort_by" column="1" />
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170 </options>
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171 <expand macro="adapter_sanitizer"/>
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172 </param>
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173 </xml>
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174
11
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175 <xml name="single_end_options" >
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176
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177 <section name="r1" title="Read 1 Options" expanded="True">
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178
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179 <repeat name="adapters" title="3' (End) Adapters" help="Sequence of an adapter ligated to the 3' end (paired data: of the first read). The adapter and subsequent bases are trimmed. If a '$' character is appended ('anchoring'), the adapter is only found if it is a suffix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below.">
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180 <conditional name="adapter_source">
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181 <param name="adapter_source_list" type="select" label="Source" >
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182 <option value="builtin" selected="True">Standard (select from the list below)</option>
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183 <option value="user">Enter custom sequence</option>
19
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184 <option value="file">File From History</option>
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185 </param>
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186
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187 <when value="user">
16
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188 <param name="adapter_name" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional if Multiple output is 'No')" />
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189 <expand macro="adapter" name="adapter" argument="-a" type="text" value="AATTGGCC" label="Enter custom 3' adapter sequence" />
11
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190 </when>
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191
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192 <when value="builtin">
22
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193 <expand macro="adapter_select" name="adapter" argument="-a" label="Choose 3' adapter"/>
11
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194 </when>
19
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195
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196 <when value="file">
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197 <param name="adapter_file" argument="-a" format="fasta" type="data" help="Should be of datatype FASTA" label="Choose file containing 3' adapters" />
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198 </when>
11
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199 </conditional>
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200 </repeat>
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201
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202 <repeat name="front_adapters" title="5' (Front) Adapters" help="Sequence of an adapter ligated to the 5' end (paired data: of the first read). The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a '^' character is prepended ('anchoring'), the adapter is only found if it is a prefix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below.">
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203 <conditional name="front_adapter_source">
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204 <param name="front_adapter_source_list" type="select" label="Source">
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205 <option value="builtin" selected="True">Standard (select from the list below)</option>
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206 <option value="user">Enter custom sequence</option>
19
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207 <option value="file">File From History</option>
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208 </param>
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209
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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210 <when value="user">
16
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211 <param name="front_adapter_name" type="text" value="" optional="True" label="Enter custom 5' adapter name (Optional if Multiple output is 'No')" />
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212 <expand macro="adapter" name="front_adapter" argument="-g" value="AATTGGCC" label="Enter custom 5' adapter sequence" />
11
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213 </when>
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214 <when value="builtin">
22
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215 <expand macro="adapter_select" name="front_adapter" argument="-g" label="Choose 5' adapter"/>
11
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216 </when>
19
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217 <when value="file">
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218 <param name="front_adapter_file" argument="-g" format="fasta" type="data" help="Should be of datatype &quot;FASTA&quot;" label="Choose file containing 5' adapters" />
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219 </when>
11
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220 </conditional>
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221 </repeat>
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222
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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223 <repeat name="anywhere_adapters" title="5' or 3' (Anywhere) Adapters" help="Sequence of an adapter that may be ligated to the 5' or 3' end (paired data: of the first read). Both types of matches as described under 3' und 5' Adapters are allowed. If the first base of the read is part of the match, the behavior is as with 5' Adapters, otherwise as with 3' Adapters. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to!">
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224 <conditional name="anywhere_adapter_source">
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225 <param name="anywhere_adapter_source_list" type="select" label="Source">
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226 <option value="builtin" selected="True">Standard (select from the list below)</option>
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227 <option value="user">Enter custom sequence</option>
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228 <option value="file">File From History</option>
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229 </param>
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230
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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231 <when value="user">
16
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232 <param name="anywhere_adapter_name" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional if Multiple output is 'No')" />
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233 <expand macro="adapter" name="anywhere_adapter" argument="-b" value="AATTGGCC" label="Enter custom 5' or 3' adapter sequence" />
11
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234 </when>
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235 <when value="builtin">
22
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236 <expand macro="adapter_select" name="anywhere_adapter" argument="-b" label="Choose 5' or 3' adapter"/>
11
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237 </when>
19
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238 <when value="file">
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239 <param name="anywhere_adapter_file" argument="-b" format="fasta" type="data" help="Should be of datatype &quot;FASTA&quot;" label="Choose file containing 3' or 5' adapters" />
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240 </when>
11
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241 </conditional>
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242 </repeat>
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243
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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244 <param name="cut" argument="-u" type="integer" value="0" optional="True" label="Cut bases from reads before adapter trimming" help="Remove bases from each read (first read only if paired). If positive, remove bases from the beginning. If negative, remove bases from the end. This is applied *before* adapter trimming." />
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245
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246 </section>
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247
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248 </xml>
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249
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250 <xml name="paired_end_options" >
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251
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252 <!-- Read 1 Options -->
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253 <expand macro="single_end_options" />
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254
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255 <!-- Read 2 Options -->
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256 <section name="r2" title="Read 2 Options" expanded="True">
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257
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258 <repeat name="adapters2" title="3' (End) Adapters" help="Sequence of an adapter ligated to the 3' end of the second read in each pair. The adapter and subsequent bases are trimmed. If a '$' character is appended ('anchoring'), the adapter is only found if it is a suffix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below.">
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259 <conditional name="adapter_source2">
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260 <param name="adapter_source_list2" type="select" label="Source" >
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261 <option value="builtin" selected="True">Standard (select from the list below)</option>
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262 <option value="user">Enter custom sequence</option>
19
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263 <option value="file">File From History</option>
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264 </param>
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265
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266 <when value="user">
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267 <param name="adapter_name2" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional)" />
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268 <expand macro="adapter" name="adapter2" argument="-A" label="Enter custom 3' adapter sequence" value="AATTGGCC" />
11
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269 </when>
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270
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271 <when value="builtin">
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272 <expand macro="adapter_select" name="adapter2" argument="-A" label="Choose 3' adapter"/>
11
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273 </when>
19
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274 <when value="file">
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275 <param name="adapter_file2" argument="-a" format="fasta" type="data" help="Should be of datatype &quot;FASTA&quot;" label="Choose file containing 3' adapters" />
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276 </when>
11
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277 </conditional>
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278 </repeat>
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279
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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280 <repeat name="front_adapters2" title="5' (Front) Adapters" help="Sequence of an adapter ligated to the 5' end of the second read in each pair. The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a '^' character is prepended ('anchoring'), the adapter is only found if it is a prefix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below.">
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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281 <conditional name="front_adapter_source2">
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282 <param name="front_adapter_source_list2" type="select" label="Source">
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283 <option value="builtin" selected="True">Standard (select from the list below)</option>
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284 <option value="user">Enter custom sequence</option>
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285 <option value="file">File From History</option>
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286 </param>
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287
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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288 <when value="user">
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289 <param name="front_adapter_name2" type="text" value="" label="Enter custom 5' adapter name (Optional)" />
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290 <expand macro="adapter" name="front_adapter2" argument="-G" value="AATTGGCC" label="Enter custom 5' adapter sequence" />
11
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291 </when>
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292 <when value="builtin">
22
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293 <expand macro="adapter_select" name="front_adapter2" argument="-G" label="Choose 5' adapter"/>
11
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294 </when>
19
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295 <when value="file">
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296 <param name="front_adapter_file2" argument="-g" format="fasta" type="data" help="Should be of datatype &quot;FASTA&quot;" label="Choose file containing 5' adapters" />
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297 </when>
11
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298 </conditional>
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299 </repeat>
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300
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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301 <repeat name="anywhere_adapters2" title="5' or 3' (Anywhere) Adapters" help="Sequence of an adapter that may be ligated to the 5' or 3' end of the second read in each pair. Both types of matches as described under under 3' und 5' Adapters are allowed. If the first base of the read is part of the match, the behavior is as with 5' Adapters, otherwise as with 3' Adapters. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to!">
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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302 <conditional name="anywhere_adapter_source2">
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303 <param name="anywhere_adapter_source_list2" type="select" label="Source">
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304 <option value="builtin" selected="True">Standard (select from the list below)</option>
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305 <option value="user">Enter custom sequence</option>
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306 <option value="file">File From History</option>
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307 </param>
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308
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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309 <when value="user">
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310 <param name="anywhere_adapter_name2" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional)" />
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311 <expand macro="adapter" name="anywhere_adapter2" argument="-B" label="Enter custom 5' or 3' adapter sequence" value="AATTGGCC" />
11
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312 </when>
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313 <when value="builtin">
22
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314 <expand macro="adapter_select" name="anywhere_adapter2" argument="-B" type="select" label="Choose 5' or 3' adapter"/>
11
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315 </when>
19
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316 <when value="file">
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317 <param name="anywhere_adapter_file2" argument="-b" format="fasta" type="data" help="Should be of datatype &quot;FASTA&quot;" label="Choose file containing 3' or 5' adapters" />
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318 </when>
11
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319 </conditional>
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320 </repeat>
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321
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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322 <param name="cut2" argument="-U" type="integer" value="0" optional="True" label="Cut bases from the second read in each pair." help="Remove bases from the beginning or end of each read before trimming adapters. If positive, the bases are removed from the beginning of each read. If negative, the bases are removed from the end of each read." />
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323
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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324 </section>
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325
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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326 </xml>
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327
12
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328 <xml name="inherit_format_1">
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329 <actions>
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330 <conditional name="library.type">
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331 <when value="single">
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332 <action type="format">
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333 <option type="from_param" name="library.input_1" param_attribute="ext" />
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334 </action>
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335 </when>
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336 <when value="paired">
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337 <action type="format">
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338 <option type="from_param" name="library.input_1" param_attribute="ext" />
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339 </action>
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340 </when>
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341 </conditional>
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342 </actions>
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343 </xml>
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344
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345 <xml name="inherit_format_2">
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346 <actions>
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347 <conditional name="library.type">
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348 <when value="paired">
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349 <action type="format">
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350 <option type="from_param" name="library.input_2" param_attribute="ext" />
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351 </action>
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352 </when>
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353 </conditional>
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354 </actions>
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355 </xml>
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356
16
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357 </macros>