annotate macros.xml @ 30:c5e2e5902201 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c75b6fda89f1cb0dce226ec983adda7f051a42e8"
author iuc
date Wed, 02 Mar 2022 08:37:02 +0000
parents 48f587c13075
children 02c5a84971c8
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1 <macros>
30
c5e2e5902201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c75b6fda89f1cb0dce226ec983adda7f051a42e8"
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2 <token name="@TOOL_VERSION@">3.7</token>
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3 <token name="@VERSION_SUFFIX@">0</token>
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44e2cc14f75b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 7cca91ac13859592f44b2f16d3aa70c28709af8d"
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4 <token name="@FASTQ_TYPES@">fastq.gz,fastq,fasta</token>
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5 <xml name="edam_ontology">
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6 <edam_topics>
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7 <edam_topic>topic_0632</edam_topic>
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8 </edam_topics>
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9 <edam_operations>
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10 <edam_operation>operation_0231</edam_operation>
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11 </edam_operations>
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12 </xml>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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13 <xml name="requirements">
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14 <requirements>
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15 <requirement type="package" version="@TOOL_VERSION@">cutadapt</requirement>
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16 </requirements>
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17 </xml>
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18 <xml name="citations">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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19 <citations>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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20 <citation type="doi">10.14806/ej.17.1.200</citation>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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21 </citations>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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22 </xml>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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23 <xml name="xrefs">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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24 <xrefs>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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25 <xref type='bio.tools'>cutadapt</xref>
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26 </xrefs>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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27 </xml>
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28 <token name="@read1_options@"><![CDATA[
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8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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30 ## Read1 trimming
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8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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32 #for $a in $library.r1.adapters
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33 #if $a.adapter_source.adapter_source_list == 'builtin':
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34 -a '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}${adapter_options.internal}${a.single_noindels}'
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35 #else if $a.adapter_source.adapter_source_list == 'file':
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36 -a file:'${a.adapter_source.adapter_file}${adapter_options.internal}${a.single_noindels}'
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37 #else if str($a.adapter_source.adapter_name) != "":
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38 -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}${adapter_options.internal}${a.single_noindels}'
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39 #else
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40 -a '${a.adapter_source.adapter}${adapter_options.internal}${a.single_noindels}'
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41 #end if
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42 #end for
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43 #for $aa in $library.r1.anywhere_adapters
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44 #if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'builtin':
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45 -b '${aa.anywhere_adapter_source.anywhere_adapter.fields.name}'='${aa.anywhere_adapter_source.anywhere_adapter}${aa.single_noindels}'
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46 #else if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'file':
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47 -b file:'${aa.anywhere_adapter_source.anywhere_adapter_file}${aa.single_noindels}'
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48 #else if str($aa.anywhere_adapter_source.anywhere_adapter_name) != "":
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49 -b '${aa.anywhere_adapter_source.anywhere_adapter_name}'='${aa.anywhere_adapter_source.anywhere_adapter}${aa.single_noindels}'
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50 #else
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51 -b '${aa.anywhere_adapter_source.anywhere_adapter}${aa.single_noindels}'
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52 #end if
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53 #end for
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54 #for $fa in $library.r1.front_adapters
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55 #if $fa.front_adapter_source.front_adapter_source_list == 'builtin':
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56 -g '${fa.front_adapter_source.front_adapter.fields.name}'='${adapter_options.internal}${fa.front_adapter_source.front_adapter}${fa.single_noindels}'
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57 #else if $fa.front_adapter_source.front_adapter_source_list == 'file':
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58 -g file:'${adapter_options.internal}${fa.front_adapter_source.front_adapter_file}${fa.single_noindels}'
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59 #else if str($fa.front_adapter_source.front_adapter_name) != "":
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60 -g '${fa.front_adapter_source.front_adapter_name}'='${adapter_options.internal}${fa.front_adapter_source.front_adapter}${fa.single_noindels}'
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61 #else
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62 -g '${adapter_options.internal}${fa.front_adapter_source.front_adapter}${fa.single_noindels}'
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63 #end if
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64 #end for
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65
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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66 #if str($library.r1.cut) != '0':
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67 -u $library.r1.cut
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68 #end if
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69
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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70 ## Additional Outputs
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71
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72 #if 'info_file' in $output_selector:
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73 --info-file=$info_file
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74 #end if
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75 #if 'rest_file' in $output_selector:
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76 --rest-file='${rest_output}'
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77 #end if
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78 #if 'wildcard_file' in $output_selector:
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79 --wildcard-file='${wild_output}'
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80 #end if
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81 #if 'too_short_file' in $output_selector:
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82 --too-short-output='${too_short_output}'
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83 #end if
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84 #if 'too_long_file' in $output_selector:
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85 --too-long-output='${too_long_output}'
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86 #end if
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87 #if 'untrimmed_file' in $output_selector:
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88 --untrimmed-output='${untrimmed_output}'
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89 #end if
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90
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91 ]]></token>
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92
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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93 <token name="@read2_options@"><![CDATA[
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94
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95 ## Read2 trimming
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96
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97 #for $a in $library.r2.adapters2
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98 #if $a.adapter_source2.adapter_source_list2 == 'builtin':
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99 -A '${a.adapter_source2.adapter2.fields.name}'='${a.adapter_source2.adapter2}${adapter_options.internal}${a.single_noindels}'
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100 #else if $a.adapter_source2.adapter_source_list2 == 'file':
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101 -A file:'${a.adapter_source2.adapter_file2}${adapter_options.internal}${a.single_noindels}'
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102 #else if str($a.adapter_source2.adapter_name2) != "":
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103 -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}${adapter_options.internal}${a.single_noindels}'
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104 #else
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105 -A '${a.adapter_source2.adapter2}${adapter_options.internal}${a.single_noindels}'
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106 #end if
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107 #end for
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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108 #for $aa in $library.r2.anywhere_adapters2
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109 #if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'builtin':
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110 -B '${aa.anywhere_adapter_source2.anywhere_adapter2.fields.name}'='${aa.anywhere_adapter_source2.anywhere_adapter2}${aa.single_noindels}'
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111 #else if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'file':
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112 -B file:'${aa.anywhere_adapter_source2.anywhere_adapter_file2}${aa.single_noindels}'
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113 #else if str($aa.anywhere_adapter_source2.anywhere_adapter_name2) != "":
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114 -B '${aa.anywhere_adapter_source2.anywhere_adapter_name2}'='${aa.anywhere_adapter_source2.anywhere_adapter2}${aa.single_noindels}'
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115 #else
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116 -B '${aa.anywhere_adapter_source2.anywhere_adapter2}'
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117 #end if
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118 #end for
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119 #for $fa in $library.r2.front_adapters2
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120 #if $fa.front_adapter_source2.front_adapter_source_list2 == 'builtin':
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121 -G '${fa.front_adapter_source2.front_adapter2.fields.name}'='${adapter_options.internal}${fa.front_adapter_source2.front_adapter2}${fa.single_noindels}'
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122 #else if $fa.front_adapter_source2.front_adapter_source_list2 == 'file':
27
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123 -G file:'${adapter_options.internal}${fa.front_adapter_source2.front_adapter_file2}${fa.single_noindels}'
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124 #else if str($fa.front_adapter_source2.front_adapter_name2) != "":
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125 -G '${fa.front_adapter_source2.front_adapter_name2}'='${adapter_options.internal}${fa.front_adapter_source2.front_adapter2}${fa.single_noindels}'
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126 #else
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diff changeset
127 -G '${adapter_options.internal}${fa.front_adapter_source2.front_adapter2}${fa.single_noindels}'
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128 #end if
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129 #end for
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130
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131 #if str($library.r2.cut2) != '0':
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132 -U $library.r2.cut2
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133 #end if
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134
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135 ## Additional Outputs - Read 2
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136
24
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137 #if 'too_short_file' in $output_selector:
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138 --too-short-paired-output='${too_short_paired_output}'
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139 #end if
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140 #if 'too_long_file' in $output_selector:
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141 --too-long-paired-output='${too_long_paired_output}'
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142 #end if
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143 #if 'untrimmed_file' in $output_selector:
20
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144 --untrimmed-paired-output='${untrimmed_paired_output}'
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145 #end if
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146
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147 ]]></token>
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148
22
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149 <xml name="adapter_sanitizer">
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150 <sanitizer>
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151 <valid initial="string.digits">
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152 <add value="A"/><!--standard nucleotides-->
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153 <add value="T"/>
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154 <add value="C"/>
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155 <add value="G"/>
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156
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157 <add value="U"/><!--ambiguous nucleotides-->
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diff changeset
158 <add value="R"/>
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159 <add value="Y"/>
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diff changeset
160 <add value="S"/>
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iuc
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diff changeset
161 <add value="W"/>
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iuc
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diff changeset
162 <add value="K"/>
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diff changeset
163 <add value="M"/>
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iuc
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diff changeset
164 <add value="B"/>
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diff changeset
165 <add value="D"/>
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iuc
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diff changeset
166 <add value="H"/>
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iuc
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diff changeset
167 <add value="V"/>
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iuc
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diff changeset
168 <add value="N"/>
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diff changeset
169
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
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170 <add value="X"/><!-- don't match any nucleotide-->
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diff changeset
171
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
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diff changeset
172 <add value="{"/><!--specify repeats .. needs digits which are added as default-->
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diff changeset
173 <add value="}"/>
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174
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175 <add value="^"/><!--anchoring-->
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176 <add value="$"/>
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177 <add value="."/>
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178 <add value="("/><!--specify what to keep-->
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179 <add value=")"/>
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180
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181 </valid>
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182 </sanitizer>
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183 </xml>
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184
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185 <xml name="adapter" token_name="" token_argument="" token_value="" token_label="">
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186 <param name="@NAME@" argument="@ARGUMENT@" type="text" value="@VALUE@" label="@LABEL@">
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187 <expand macro="adapter_sanitizer"/>
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188 </param>
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189 </xml>
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190
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
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191 <xml name="adapter_select" token_name="" token_argument="" token_label="">
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192 <param name="@NAME@" argument="@ARGUMENT@" type="select" label="@LABEL@">
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193 <options from_data_table="adapters">
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194 <filter type="sort_by" column="1" />
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195 </options>
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196 <expand macro="adapter_sanitizer"/>
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197 </param>
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198 </xml>
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199
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200 <xml name="single_end_options" >
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201
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202 <section name="r1" title="Read 1 Options" expanded="True">
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203
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204 <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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205 <conditional name="adapter_source">
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206 <param name="adapter_source_list" type="select" label="Source" >
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207 <option value="builtin" selected="True">Standard (select from the list below)</option>
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208 <option value="user">Enter custom sequence</option>
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209 <option value="file">File from history</option>
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210 </param>
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211
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212 <when value="user">
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213 <param name="adapter_name" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional if Multiple output is 'No')" />
22
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214 <expand macro="adapter" name="adapter" argument="-a" type="text" value="AATTGGCC" label="Enter custom 3' adapter sequence" />
11
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215 </when>
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216
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217 <when value="builtin">
22
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218 <expand macro="adapter_select" name="adapter" argument="-a" label="Choose 3' adapter"/>
11
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219 </when>
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220
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221 <when value="file">
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222 <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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223 </when>
11
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224 </conditional>
27
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225 <param name="single_noindels" type="boolean" truevalue=";noindels" falsevalue="" checked="false" label="Disallow indels for this adapter"/>
11
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226 </repeat>
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227
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228 <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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229 <conditional name="front_adapter_source">
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230 <param name="front_adapter_source_list" type="select" label="Source">
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231 <option value="builtin" selected="True">Standard (select from the list below)</option>
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232 <option value="user">Enter custom sequence</option>
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233 <option value="file">File from history</option>
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234 </param>
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235
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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236 <when value="user">
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237 <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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238 <expand macro="adapter" name="front_adapter" argument="-g" value="AATTGGCC" label="Enter custom 5' adapter sequence" />
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239 </when>
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240 <when value="builtin">
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241 <expand macro="adapter_select" name="front_adapter" argument="-g" label="Choose 5' adapter"/>
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242 </when>
19
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243 <when value="file">
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244 <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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245 </when>
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246 </conditional>
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247 <param name="single_noindels" type="boolean" truevalue=";noindels" falsevalue="" checked="false" label="Disallow indels for this adapter"/>
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248 </repeat>
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249
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250 <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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251 <conditional name="anywhere_adapter_source">
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252 <param name="anywhere_adapter_source_list" type="select" label="Source">
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253 <option value="builtin" selected="True">Standard (select from the list below)</option>
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254 <option value="user">Enter custom sequence</option>
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255 <option value="file">File from history</option>
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256 </param>
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257
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258 <when value="user">
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259 <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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260 <expand macro="adapter" name="anywhere_adapter" argument="-b" value="AATTGGCC" label="Enter custom 5' or 3' adapter sequence" />
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261 </when>
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262 <when value="builtin">
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263 <expand macro="adapter_select" name="anywhere_adapter" argument="-b" label="Choose 5' or 3' adapter"/>
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264 </when>
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265 <when value="file">
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266 <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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267 </when>
11
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268 </conditional>
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269 <param name="single_noindels" type="boolean" truevalue=";noindels" falsevalue="" checked="false" label="Disallow indels for this adapter"/>
11
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270 </repeat>
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271
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272 <param argument="--cut" 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." />
11
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273
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274 </section>
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275
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276 </xml>
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277
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278 <xml name="paired_end_options" >
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279
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280 <!-- Read 1 Options -->
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281 <expand macro="single_end_options" />
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282
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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283 <!-- Read 2 Options -->
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284 <section name="r2" title="Read 2 Options" expanded="True">
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285
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286 <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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287 <conditional name="adapter_source2">
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288 <param name="adapter_source_list2" type="select" label="Source" >
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289 <option value="builtin" selected="True">Standard (select from the list below)</option>
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290 <option value="user">Enter custom sequence</option>
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291 <option value="file">File from history</option>
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292 </param>
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293
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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294 <when value="user">
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295 <param name="adapter_name2" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional)" />
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296 <expand macro="adapter" name="adapter2" argument="-A" label="Enter custom 3' adapter sequence" value="AATTGGCC" />
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297 </when>
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298
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299 <when value="builtin">
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300 <expand macro="adapter_select" name="adapter2" argument="-A" label="Choose 3' adapter"/>
11
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301 </when>
19
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302 <when value="file">
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303 <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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304 </when>
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305 </conditional>
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306 <param name="single_noindels" type="boolean" truevalue=";noindels" falsevalue="" checked="false" label="Disallow indels for this adapter"/>
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307 </repeat>
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308
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309 <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.">
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310 <conditional name="front_adapter_source2">
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311 <param name="front_adapter_source_list2" type="select" label="Source">
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312 <option value="builtin" selected="True">Standard (select from the list below)</option>
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313 <option value="user">Enter custom sequence</option>
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314 <option value="file">File from history</option>
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315 </param>
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316
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317 <when value="user">
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318 <param name="front_adapter_name2" type="text" value="" label="Enter custom 5' adapter name (Optional)" />
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319 <expand macro="adapter" name="front_adapter2" argument="-G" value="AATTGGCC" label="Enter custom 5' adapter sequence" />
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320 </when>
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321 <when value="builtin">
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322 <expand macro="adapter_select" name="front_adapter2" argument="-G" label="Choose 5' adapter"/>
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323 </when>
19
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324 <when value="file">
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325 <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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326 </when>
11
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327 </conditional>
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328 <param name="single_noindels" type="boolean" truevalue=";noindels" falsevalue="" checked="false" label="Disallow indels for this adapter"/>
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329 </repeat>
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330
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331 <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!">
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332 <conditional name="anywhere_adapter_source2">
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333 <param name="anywhere_adapter_source_list2" type="select" label="Source">
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334 <option value="builtin" selected="True">Standard (select from the list below)</option>
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335 <option value="user">Enter custom sequence</option>
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336 <option value="file">File from history</option>
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337 </param>
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338
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339 <when value="user">
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340 <param name="anywhere_adapter_name2" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional)" />
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341 <expand macro="adapter" name="anywhere_adapter2" argument="-B" label="Enter custom 5' or 3' adapter sequence" value="AATTGGCC" />
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342 </when>
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343 <when value="builtin">
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344 <expand macro="adapter_select" name="anywhere_adapter2" argument="-B" type="select" label="Choose 5' or 3' adapter"/>
11
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345 </when>
19
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346 <when value="file">
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347 <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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348 </when>
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349 </conditional>
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350 <param name="single_noindels" type="boolean" truevalue=";noindels" falsevalue="" checked="false" label="Disallow indels for this adapter"/>
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351 </repeat>
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352
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353 <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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de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
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354 <param name="quality_cutoff2" type="text" optional="true" label="Optional separate quality cutoff for Read 2" help="Trim low-quality bases from 5' and/or 3' ends of each read before adapter removal. If one value is given, only the 3' end is trimmed. If two comma-separated cutoffs are given, the 5' end is trimmed with the first cutoff, the 3' end with the second. Leave blank to use the same value as for Read 1">
de6cebe3c043 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
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355 <sanitizer>
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356 <valid initial="string.digits"><add value="," /></valid>
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357 </sanitizer>
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358 <validator type="regex">[0-9,]+</validator>
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359 </param>
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360 </section>
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361
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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362 </xml>
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363
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364 <xml name="inherit_format_1">
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365 <actions>
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366 <conditional name="library.type">
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367 <when value="single">
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368 <action type="format">
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369 <option type="from_param" name="library.input_1" param_attribute="ext" />
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370 </action>
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371 </when>
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372 <when value="paired">
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373 <action type="format">
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374 <option type="from_param" name="library.input_1" param_attribute="ext" />
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375 </action>
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376 </when>
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377 </conditional>
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378 </actions>
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379 </xml>
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380
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381 <xml name="inherit_format_2">
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382 <actions>
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383 <conditional name="library.type">
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384 <when value="paired">
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385 <action type="format">
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386 <option type="from_param" name="library.input_2" param_attribute="ext" />
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387 </action>
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388 </when>
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389 </conditional>
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390 </actions>
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391 </xml>
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392
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393 </macros>