Mercurial > repos > lparsons > cutadapt

annotate macros.xml @ 24:288f97432497 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
author iuc
date Wed, 02 Jun 2021 22:47:34 +0000
parents c4b82dce8335
children 4e5056fefd88
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rev   line source
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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1 <macros>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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2 <token name="@TOOL_VERSION@">3.4</token>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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3 <token name="@GALAXY_TOOL_VERSION@">galaxy0</token>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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4 <xml name="edam_ontology">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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5 <edam_topics>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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6 <edam_topic>topic_0632</edam_topic>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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7 </edam_topics>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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8 <edam_operations>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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9 <edam_operation>operation_0231</edam_operation>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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10 </edam_operations>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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11 </xml>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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12 <xml name="requirements">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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13 <requirements>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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14 <requirement type="package" version="@TOOL_VERSION@">cutadapt</requirement>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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15 </requirements>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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16 </xml>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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17 <xml name="citations">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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18 <citations>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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19 <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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20 </citations>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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21 </xml>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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22 <xml name="xrefs">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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23 <xrefs>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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24 <xref type='bio.tools'>cutadapt</xref>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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25 </xrefs>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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26 </xml>
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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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27 <token name="@read1_options@"><![CDATA[
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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28
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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29 ## Read1 trimming
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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30
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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31 #for $a in $library.r1.adapters
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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32 #if $a.adapter_source.adapter_source_list == 'builtin':
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33 -a '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}${adapter_options.internal}'
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34 #else if $a.adapter_source.adapter_source_list == 'file':
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35 -a file:'${a.adapter_source.adapter_file}${adapter_options.internal}'
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36 #else if str($a.adapter_source.adapter_name) != "":
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37 -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}${adapter_options.internal}'
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8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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38 #else
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288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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39 -a '${a.adapter_source.adapter}${adapter_options.internal}'
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40 #end if
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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41 #end for
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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42 #for $aa in $library.r1.anywhere_adapters
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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43 #if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'builtin':
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44 -b '${aa.anywhere_adapter_source.anywhere_adapter.fields.name}'='${aa.anywhere_adapter_source.anywhere_adapter}'
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45 #else if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'file':
49370cb85f0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969
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46 -b file:'${aa.anywhere_adapter_source.anywhere_adapter_file}'
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47 #else if str($aa.anywhere_adapter_source.anywhere_adapter_name) != "":
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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48 -b '${aa.anywhere_adapter_source.anywhere_adapter_name}'='${aa.anywhere_adapter_source.anywhere_adapter}'
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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49 #else
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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50 -b '${aa.anywhere_adapter_source.anywhere_adapter}'
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51 #end if
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52 #end for
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53 #for $fa in $library.r1.front_adapters
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54 #if $fa.front_adapter_source.front_adapter_source_list == 'builtin':
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55 -g '${fa.front_adapter_source.front_adapter.fields.name}'='${adapter_options.internal}${fa.front_adapter_source.front_adapter}'
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56 #else if $fa.front_adapter_source.front_adapter_source_list == 'file':
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57 -g file:'${adapter_options.internal}${fa.front_adapter_source.front_adapter_file}'
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58 #else if str($fa.front_adapter_source.front_adapter_name) != "":
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59 -g '${fa.front_adapter_source.front_adapter_name}'='${adapter_options.internal}${fa.front_adapter_source.front_adapter}'
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8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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60 #else
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61 -g '${adapter_options.internal}${fa.front_adapter_source.front_adapter}'
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62 #end if
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63 #end for
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64
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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65 #if str($library.r1.cut) != '0':
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66 -u $library.r1.cut
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67 #end if
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68
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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69 ## Additional Outputs
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70
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71 #if 'info_file' in $output_selector:
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72 --info-file=$info_file
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73 #end if
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74 #if 'rest_file' in $output_selector:
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75 --rest-file='${rest_output}'
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76 #end if
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77 #if 'wildcard_file' in $output_selector:
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78 --wildcard-file='${wild_output}'
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79 #end if
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80 #if 'too_short_file' in $output_selector:
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81 --too-short-output='${too_short_output}'
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82 #end if
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83 #if 'too_long_file' in $output_selector:
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84 --too-long-output='${too_long_output}'
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85 #end if
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86 #if 'untrimmed_file' in $output_selector:
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87 --untrimmed-output='${untrimmed_output}'
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88 #end if
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89
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90 ]]></token>
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91
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92 <token name="@read2_options@"><![CDATA[
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93
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94 ## Read2 trimming
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95
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96 #for $a in $library.r2.adapters2
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97 #if $a.adapter_source2.adapter_source_list2 == 'builtin':
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98 -A '${a.adapter_source2.adapter2.fields.name}'='${a.adapter_source2.adapter2}${adapter_options.internal}'
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99 #else if $a.adapter_source2.adapter_source_list2 == 'file':
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100 -A file:'${a.adapter_source2.adapter_file2}${adapter_options.internal}'
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101 #else if str($a.adapter_source2.adapter_name2) != "":
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102 -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}${adapter_options.internal}'
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103 #else
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104 -A '${a.adapter_source2.adapter2}${adapter_options.internal}'
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105 #end if
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106 #end for
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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107 #for $aa in $library.r2.anywhere_adapters2
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108 #if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'builtin':
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109 -B '${aa.anywhere_adapter_source2.anywhere_adapter2.fields.name}'='${aa.anywhere_adapter_source2.anywhere_adapter2}'
19
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110 #else if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'file':
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111 -B file:'${aa.anywhere_adapter_source2.anywhere_adapter_file2}'
11
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112 #else if str($aa.anywhere_adapter_source2.anywhere_adapter_name2) != "":
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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113 -B '${aa.anywhere_adapter_source2.anywhere_adapter_name2}'='${aa.anywhere_adapter_source2.anywhere_adapter2}'
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114 #else
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115 -B '${aa.anywhere_adapter_source2.anywhere_adapter2}'
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116 #end if
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117 #end for
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118 #for $fa in $library.r2.front_adapters2
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119 #if $fa.front_adapter_source2.front_adapter_source_list2 == 'builtin':
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120 -G '${fa.front_adapter_source2.front_adapter2.fields.name}'='${adapter_options.internal}${fa.front_adapter_source2.front_adapter2}'
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121 #else if $fa.front_adapter_source2.front_adapter_source_list2 == 'file':
24
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122 -G file:'${adapter_options.internal}${fa.front_adapter_source2.front_adapter_file2}'
11
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123 #else if str($fa.front_adapter_source2.front_adapter_name2) != "":
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124 -G '${fa.front_adapter_source2.front_adapter_name2}'='${adapter_options.internal}${fa.front_adapter_source2.front_adapter2}'
11
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125 #else
24
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126 -G '${adapter_options.internal}${fa.front_adapter_source2.front_adapter2}'
11
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127 #end if
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128 #end for
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129
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130 #if str($library.r2.cut2) != '0':
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diff changeset
131 -U $library.r2.cut2
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132 #end if
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133
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134 ## Additional Outputs - Read 2
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135
24
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136 #if 'too_short_file' in $output_selector:
20
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137 --too-short-paired-output='${too_short_paired_output}'
11
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138 #end if
24
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139 #if 'too_long_file' in $output_selector:
20
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140 --too-long-paired-output='${too_long_paired_output}'
11
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141 #end if
24
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142 #if 'untrimmed_file' in $output_selector:
20
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143 --untrimmed-paired-output='${untrimmed_paired_output}'
11
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144 #end if
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145
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146 ]]></token>
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147
22
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148 <xml name="adapter_sanitizer">
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149 <sanitizer>
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150 <valid initial="string.digits">
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151 <add value="A"/><!--standard nucleotides-->
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
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diff changeset
152 <add value="T"/>
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153 <add value="C"/>
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154 <add value="G"/>
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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 <add value="U"/><!--ambiguous nucleotides-->
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
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diff changeset
157 <add value="R"/>
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158 <add value="Y"/>
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159 <add value="S"/>
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diff changeset
160 <add value="W"/>
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iuc
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diff changeset
161 <add value="K"/>
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
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diff changeset
162 <add value="M"/>
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
iuc
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diff changeset
163 <add value="B"/>
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
iuc
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diff changeset
164 <add value="D"/>
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
iuc
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diff changeset
165 <add value="H"/>
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iuc
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diff changeset
166 <add value="V"/>
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
iuc
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diff changeset
167 <add value="N"/>
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diff changeset
168
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
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diff changeset
169 <add value="X"/><!-- don't match any nucleotide-->
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
iuc
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diff changeset
170
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
iuc
parents: 20
diff changeset
171 <add value="{"/><!--specify repeats .. needs digits which are added as default-->
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
iuc
parents: 20
diff changeset
172 <add value="}"/>
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iuc
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diff changeset
173
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
iuc
parents: 20
diff changeset
174 <add value="^"/><!--anchoring-->
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
iuc
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diff changeset
175 <add value="$"/>
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
iuc
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diff changeset
176 <add value="."/>
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iuc
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diff changeset
177 <add value="("/><!--specify what to keep-->
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iuc
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178 <add value=")"/>
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179
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180 </valid>
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181 </sanitizer>
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182 </xml>
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183
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184 <xml name="adapter" token_name="" token_argument="" token_value="" token_label="">
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185 <param name="@NAME@" argument="@ARGUMENT@" type="text" value="@VALUE@" label="@LABEL@">
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186 <expand macro="adapter_sanitizer"/>
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187 </param>
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188 </xml>
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189
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190 <xml name="adapter_select" token_name="" token_argument="" token_label="">
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191 <param name="@NAME@" argument="@ARGUMENT@" type="select" label="@LABEL@">
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192 <options from_data_table="adapters">
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193 <filter type="sort_by" column="1" />
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194 </options>
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195 <expand macro="adapter_sanitizer"/>
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196 </param>
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197 </xml>
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198
11
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199 <xml name="single_end_options" >
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200
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201 <section name="r1" title="Read 1 Options" expanded="True">
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202
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203 <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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204 <conditional name="adapter_source">
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205 <param name="adapter_source_list" type="select" label="Source" >
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206 <option value="builtin" selected="True">Standard (select from the list below)</option>
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207 <option value="user">Enter custom sequence</option>
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208 <option value="file">File from history</option>
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209 </param>
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210
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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211 <when value="user">
16
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212 <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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213 <expand macro="adapter" name="adapter" argument="-a" type="text" value="AATTGGCC" label="Enter custom 3' adapter sequence" />
11
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214 </when>
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215
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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216 <when value="builtin">
22
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217 <expand macro="adapter_select" name="adapter" argument="-a" label="Choose 3' adapter"/>
11
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218 </when>
19
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219
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220 <when value="file">
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221 <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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222 </when>
11
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223 </conditional>
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224 </repeat>
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225
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226 <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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227 <conditional name="front_adapter_source">
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228 <param name="front_adapter_source_list" type="select" label="Source">
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229 <option value="builtin" selected="True">Standard (select from the list below)</option>
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230 <option value="user">Enter custom sequence</option>
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231 <option value="file">File from history</option>
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232 </param>
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233
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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234 <when value="user">
16
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235 <param name="front_adapter_name" type="text" value="" optional="True" label="Enter custom 5' adapter name (Optional if Multiple output is 'No')" />
22
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236 <expand macro="adapter" name="front_adapter" argument="-g" value="AATTGGCC" label="Enter custom 5' adapter sequence" />
11
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237 </when>
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238 <when value="builtin">
22
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239 <expand macro="adapter_select" name="front_adapter" argument="-g" label="Choose 5' adapter"/>
11
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240 </when>
19
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241 <when value="file">
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242 <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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243 </when>
11
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244 </conditional>
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245 </repeat>
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246
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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247 <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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248 <conditional name="anywhere_adapter_source">
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249 <param name="anywhere_adapter_source_list" type="select" label="Source">
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250 <option value="builtin" selected="True">Standard (select from the list below)</option>
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251 <option value="user">Enter custom sequence</option>
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252 <option value="file">File from history</option>
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253 </param>
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254
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255 <when value="user">
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256 <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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257 <expand macro="adapter" name="anywhere_adapter" argument="-b" value="AATTGGCC" label="Enter custom 5' or 3' adapter sequence" />
11
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258 </when>
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259 <when value="builtin">
22
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260 <expand macro="adapter_select" name="anywhere_adapter" argument="-b" label="Choose 5' or 3' adapter"/>
11
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261 </when>
19
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262 <when value="file">
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263 <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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264 </when>
11
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265 </conditional>
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266 </repeat>
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267
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268 <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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269
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270 </section>
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271
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272 </xml>
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273
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274 <xml name="paired_end_options" >
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275
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276 <!-- Read 1 Options -->
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277 <expand macro="single_end_options" />
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278
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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279 <!-- Read 2 Options -->
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280 <section name="r2" title="Read 2 Options" expanded="True">
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281
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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282 <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.">
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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283 <conditional name="adapter_source2">
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284 <param name="adapter_source_list2" type="select" label="Source" >
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285 <option value="builtin" selected="True">Standard (select from the list below)</option>
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286 <option value="user">Enter custom sequence</option>
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287 <option value="file">File from history</option>
11
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288 </param>
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289
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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290 <when value="user">
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291 <param name="adapter_name2" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional)" />
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292 <expand macro="adapter" name="adapter2" argument="-A" label="Enter custom 3' adapter sequence" value="AATTGGCC" />
11
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293 </when>
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294
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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295 <when value="builtin">
22
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296 <expand macro="adapter_select" name="adapter2" argument="-A" label="Choose 3' adapter"/>
11
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297 </when>
19
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298 <when value="file">
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299 <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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300 </when>
11
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301 </conditional>
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302 </repeat>
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303
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304 <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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305 <conditional name="front_adapter_source2">
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306 <param name="front_adapter_source_list2" type="select" label="Source">
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307 <option value="builtin" selected="True">Standard (select from the list below)</option>
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308 <option value="user">Enter custom sequence</option>
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309 <option value="file">File from history</option>
11
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310 </param>
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311
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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312 <when value="user">
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313 <param name="front_adapter_name2" type="text" value="" label="Enter custom 5' adapter name (Optional)" />
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314 <expand macro="adapter" name="front_adapter2" argument="-G" value="AATTGGCC" label="Enter custom 5' adapter sequence" />
11
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315 </when>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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316 <when value="builtin">
22
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317 <expand macro="adapter_select" name="front_adapter2" argument="-G" label="Choose 5' adapter"/>
11
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318 </when>
19
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319 <when value="file">
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320 <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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321 </when>
11
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322 </conditional>
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323 </repeat>
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324
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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325 <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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326 <conditional name="anywhere_adapter_source2">
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327 <param name="anywhere_adapter_source_list2" type="select" label="Source">
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328 <option value="builtin" selected="True">Standard (select from the list below)</option>
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329 <option value="user">Enter custom sequence</option>
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330 <option value="file">File from history</option>
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331 </param>
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332
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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333 <when value="user">
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334 <param name="anywhere_adapter_name2" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional)" />
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335 <expand macro="adapter" name="anywhere_adapter2" argument="-B" label="Enter custom 5' or 3' adapter sequence" value="AATTGGCC" />
11
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336 </when>
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337 <when value="builtin">
22
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338 <expand macro="adapter_select" name="anywhere_adapter2" argument="-B" type="select" label="Choose 5' or 3' adapter"/>
11
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339 </when>
19
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340 <when value="file">
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341 <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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342 </when>
11
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343 </conditional>
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344 </repeat>
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345
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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346 <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." />
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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347
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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348 </section>
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349
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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350 </xml>
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351
12
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352 <xml name="inherit_format_1">
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353 <actions>
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354 <conditional name="library.type">
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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355 <when value="single">
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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356 <action type="format">
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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357 <option type="from_param" name="library.input_1" param_attribute="ext" />
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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358 </action>
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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359 </when>
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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parents: 11
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360 <when value="paired">
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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parents: 11
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361 <action type="format">
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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362 <option type="from_param" name="library.input_1" param_attribute="ext" />
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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363 </action>
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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364 </when>
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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365 </conditional>
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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366 </actions>
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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367 </xml>
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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368
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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369 <xml name="inherit_format_2">
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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370 <actions>
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
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371 <conditional name="library.type">
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
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372 <when value="paired">
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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parents: 11
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373 <action type="format">
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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374 <option type="from_param" name="library.input_2" param_attribute="ext" />
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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375 </action>
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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376 </when>
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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377 </conditional>
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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378 </actions>
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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379 </xml>
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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380
16
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
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381 </macros>