Mercurial > repos > devteam > fastq_manipulation
annotate fastq_manipulation.xml @ 4:6f864b826b3e draft
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit 31edb920789fbd080260f853bc856be72fa7cfa8"
author | devteam |
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date | Fri, 01 Nov 2019 13:17:24 -0400 |
parents | 7ea141c4c834 |
children | b77ecfa1664e |
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7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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1 <tool id="fastq_manipulation" name="Manipulate FASTQ" version="1.1.1"> |
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6f864b826b3e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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2 <options sanitize="false" /> |
6f864b826b3e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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3 <!-- This tool uses a file to rely all parameter information (actually a dynamically generated python module), we can safely not sanitize any parameters --> |
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7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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4 <description>reads on various attributes</description> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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5 <requirements> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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6 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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7 </requirements> |
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6f864b826b3e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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8 <edam_topics> |
6f864b826b3e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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9 <edam_topic>topic_0622</edam_topic> |
6f864b826b3e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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10 </edam_topics> |
6f864b826b3e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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11 <edam_operations> |
6f864b826b3e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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12 <edam_operation>operation_0233</edam_operation> |
6f864b826b3e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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13 </edam_operations> |
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7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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14 <command><![CDATA[ |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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15 gx-fastq-manipulation '$input_file' '$fastq_manipulation_file' '$output_file' '$output_file.files_path' '${input_file.extension[len('fastq'):]}' |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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16 ]]></command> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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17 <configfiles> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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18 <configfile name="fastq_manipulation_file"><![CDATA[##create an importable module |
0 | 19 #import binascii |
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7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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20 import binascii |
0 | 21 import re |
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7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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22 import six |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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23 |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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24 if six.PY2: |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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25 from string import maketrans |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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26 else: |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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27 maketrans = str.maketrans |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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28 |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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29 |
0 | 30 ##does read match |
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7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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31 def match_read(fastq_read): |
0 | 32 #for $match_block in $match_blocks: |
33 #if $match_block['match_type']['match_type_selector'] == 'identifier': | |
3
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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34 search_target = fastq_read.identifier[1:] ##don't include @ |
0 | 35 #elif $match_block['match_type']['match_type_selector'] == 'sequence': |
36 search_target = fastq_read.sequence | |
37 #elif $match_block['match_type']['match_type_selector'] == 'quality': | |
38 search_target = fastq_read.quality | |
39 #else: | |
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7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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40 #continue |
0 | 41 #end if |
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7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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42 if not re.search(binascii.unhexlify("${ binascii.hexlify(str(match_block['match_type']['match']['match_by'])) }").decode(), search_target): |
0 | 43 return False |
44 #end for | |
45 return True | |
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7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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46 |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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47 |
0 | 48 ##modify matched reads |
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7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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49 def manipulate_read(fastq_read): |
0 | 50 new_read = fastq_read.clone() |
51 #for $manipulate_block in $manipulate_blocks: | |
52 #if $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'identifier': | |
53 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'translate': | |
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7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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54 new_read.identifier = "@%s" % new_read.identifier[1:].translate(maketrans(binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from'])) }").decode(), binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to'])) }").decode())) |
0 | 55 #end if |
56 #elif $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'sequence': | |
57 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'translate': | |
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7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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58 new_read.sequence = new_read.sequence.translate(maketrans(binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from'])) }").decode(), binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to'])) }").decode())) |
0 | 59 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'rev_comp': |
60 new_read = new_read.reverse_complement() | |
61 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'rev_no_comp': | |
62 new_read = new_read.reverse() | |
63 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'no_rev_comp': | |
64 new_read = new_read.complement() | |
65 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'trim': | |
66 #if $manipulate_block['manipulation_type']['manipulation']['offset_type']['base_offset_type'] == 'offsets_percent': | |
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7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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67 left_column_offset = int(round(float(${ manipulate_block['manipulation_type']['manipulation']['offset_type']['left_column_offset'] }) / 100.0 * float(len(new_read)))) |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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68 right_column_offset = int(round(float(${ manipulate_block['manipulation_type']['manipulation']['offset_type']['right_column_offset'] }) / 100.0 * float(len(new_read)))) |
0 | 69 #else |
70 left_column_offset = ${ manipulate_block['manipulation_type']['manipulation']['offset_type']['left_column_offset'] } | |
71 right_column_offset = ${ manipulate_block['manipulation_type']['manipulation']['offset_type']['right_column_offset'] } | |
72 #end if | |
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16d28d67ebeb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
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73 if right_column_offset != 0: |
0 | 74 right_column_offset = -right_column_offset |
75 else: | |
76 right_column_offset = None | |
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7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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77 new_read = new_read.slice(left_column_offset, right_column_offset) |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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78 if not (${str(manipulate_block['manipulation_type']['manipulation']['keep_zero_length']) == 'keep_zero_length'} or len(new_read)): |
0 | 79 return None |
80 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'dna_to_rna': | |
81 new_read = new_read.sequence_as_DNA() | |
82 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'rna_to_dna': | |
83 new_read = new_read.sequence_as_RNA() | |
84 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'change_adapter': | |
85 if new_read.sequence_space == 'color': | |
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7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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86 new_read = new_read.change_adapter(binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['new_adapter'])) }").decode()) |
0 | 87 #end if |
88 #elif $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'quality': | |
89 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'translate': | |
3
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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90 new_read.quality = new_read.quality.translate(maketrans(binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from'])) }").decode(), binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to'])) }").decode())) |
0 | 91 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'map_score': |
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7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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92 def score_method(score): |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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93 raise Exception("Unimplemented") ##This option is not yet available, need to abstract out e.g. column adding tool action: preventing users from using 'harmful' actions |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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94 new_read.quality_map(score_method) |
0 | 95 #end if |
96 #elif $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'miscellaneous': | |
97 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'remove': | |
98 return None | |
99 #end if | |
100 #else: | |
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7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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101 #continue |
0 | 102 #end if |
103 #end for | |
104 if new_read.description != "+": | |
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7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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105 new_read.description = "+%s" % new_read.identifier[1:] ##ensure description is still valid |
0 | 106 return new_read |
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7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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107 |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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108 |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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109 def match_and_manipulate_read(fastq_read): |
0 | 110 new_read = fastq_read |
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7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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111 if match_read(fastq_read): |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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112 new_read = manipulate_read(fastq_read) |
0 | 113 return new_read |
3
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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114 ]]></configfile> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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changeset
|
115 </configfiles> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
116 <inputs> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
117 <!-- This tool is purposely over-engineered (e.g. Single option conditionals) to allow easy enhancement with workflow/rerun compatibility --> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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118 <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ File" help="Requires groomed data: if your data does not appear here try using the FASTQ groomer"/> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
119 <!-- Match Reads --> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
120 <repeat name="match_blocks" title="Match Reads"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
121 <conditional name="match_type"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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parents:
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changeset
|
122 <param name="match_type_selector" type="select" label="Match Reads by"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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diff
changeset
|
123 <option value="identifier">Name/Identifier</option> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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parents:
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changeset
|
124 <option value="sequence">Sequence Content</option> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
125 <option value="quality">Quality Score Content</option> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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126 </param> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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127 <when value="identifier"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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128 <conditional name="match"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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129 <param name="match_selector" type="select" label="Identifier Match Type"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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130 <option value="regex">Regular Expression</option> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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131 </param> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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132 <when value="regex"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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133 <param name="match_by" type="text" value=".*" label="Match by" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
134 </when> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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135 </conditional> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
136 </when> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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137 <when value="sequence"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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138 <conditional name="match"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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parents:
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changeset
|
139 <param name="match_selector" type="select" label="Sequence Match Type"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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parents:
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changeset
|
140 <option value="regex">Regular Expression</option> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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parents:
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changeset
|
141 </param> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
142 <when value="regex"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
143 <param name="match_by" type="text" value=".*" label="Match by" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
144 </when> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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parents:
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changeset
|
145 </conditional> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
146 </when> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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147 <when value="quality"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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148 <conditional name="match"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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149 <param name="match_selector" type="select" label="Quality Match Type"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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parents:
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changeset
|
150 <option value="regex">Regular Expression</option> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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parents:
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changeset
|
151 </param> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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parents:
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changeset
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152 <when value="regex"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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parents:
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changeset
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153 <param name="match_by" type="text" value=".*" label="Match by" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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parents:
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changeset
|
154 </when> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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parents:
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changeset
|
155 </conditional> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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parents:
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156 </when> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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parents:
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157 </conditional> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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parents:
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changeset
|
158 </repeat> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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159 <!-- Manipulate Matched Reads --> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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parents:
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changeset
|
160 <repeat name="manipulate_blocks" title="Manipulate Reads"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
161 <conditional name="manipulation_type"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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162 <param name="manipulation_type_selector" type="select" label="Manipulate Reads on"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
163 <option value="identifier">Name/Identifier</option> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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|
164 <option value="sequence">Sequence Content</option> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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165 <option value="quality">Quality Score Content</option> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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166 <option value="miscellaneous">Miscellaneous Actions</option> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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167 </param> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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168 <when value="identifier"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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169 <conditional name="manipulation"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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170 <param name="manipulation_selector" type="select" label="Identifier Manipulation Type"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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171 <option value="translate">String Translate</option> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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172 </param> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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173 <when value="translate"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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parents:
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changeset
|
174 <param name="from" type="text" value="" label="From" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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175 <param name="to" type="text" value="" label="To" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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176 </when> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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177 </conditional> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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178 </when> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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179 <when value="sequence"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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180 <conditional name="manipulation"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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181 <param name="manipulation_selector" type="select" label="Sequence Manipulation Type"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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182 <option value="rev_comp">Reverse Complement</option> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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183 <option value="rev_no_comp">Reverse, No Complement</option> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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184 <option value="no_rev_comp">Complement, No Reverse</option> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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185 <option value="trim">Trim</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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186 <option value="dna_to_rna">DNA to RNA</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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187 <option value="rna_to_dna">RNA to DNA</option> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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188 <option value="translate">String Translate</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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189 <option value="change_adapter">Change Adapter Base</option> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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190 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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191 <when value="rev_comp" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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192 <when value="rev_no_comp" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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193 <when value="no_rev_comp" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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194 <when value="trim"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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195 <conditional name="offset_type"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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196 <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Use Absolute for fixed length reads (Illumina, SOLiD)<br>Use Percentage for variable length reads (Roche/454)"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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197 <option value="offsets_absolute" selected="true">Absolute Values</option> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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198 <option value="offsets_percent">Percentage of Read Length</option> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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199 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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200 <when value="offsets_absolute"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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201 <param name="left_column_offset" type="integer" min="0" value="0" label="Offset from 5' end" help="Values start at 0, increasing from the left" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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202 <param name="right_column_offset" type="integer" value="0" label="Offset from 3' end" help="Values start at 0, increasing from the right; use a negative value to remove everything to the right of the absolute value of the position" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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203 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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204 <when value="offsets_percent"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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205 <param name="left_column_offset" type="float" min="0" max="100" value="0" label="Offset from 5' end" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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206 <param name="right_column_offset" type="float" min="0" max="100" value="0" label="Offset from 3' end" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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207 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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208 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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209 <param name="keep_zero_length" type="boolean" truevalue="keep_zero_length" falsevalue="exclude_zero_length" checked="false" label="Keep reads with zero length" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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210 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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211 <when value="dna_to_rna" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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212 <when value="rna_to_dna" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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213 <when value="translate"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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214 <param name="from" type="text" value="" label="From" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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215 <param name="to" type="text" value="" label="To" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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216 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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217 <when value="change_adapter"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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218 <param name="new_adapter" type="text" value="G" label="New adapter" help="An empty string will remove the adapter base" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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219 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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220 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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221 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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222 <when value="quality"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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223 <conditional name="manipulation"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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224 <param name="manipulation_selector" type="select" label="Quality Manipulation Type"> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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225 <option value="translate">String Translate</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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226 <!-- <option value="modify_each_score">Apply Transformation to each Score</option> Not enabled yet--> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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227 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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228 <when value="translate"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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229 <param name="from" type="text" value="" label="From" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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230 <param name="to" type="text" value="" label="To" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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231 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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232 <!-- <when value="modify_each_score"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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233 <param name="map_score" type="text" label="Modify Score by" value="$score + 1" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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234 </when> --> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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235 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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236 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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237 <when value="miscellaneous"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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238 <conditional name="manipulation"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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239 <param name="manipulation_selector" type="select" label="Miscellaneous Manipulation Type"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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240 <option value="remove">Remove Read</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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241 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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242 <when value="remove" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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243 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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244 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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245 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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246 </repeat> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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247 </inputs> |
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248 <outputs> |
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249 <data name="output_file" format_source="input_file" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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250 </outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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251 <tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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252 <!-- match all and do nothing --> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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253 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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254 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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255 <param name="match_type_selector" value="identifier" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
256 <param name="match_selector" value="regex" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
257 <param name="match_by" value=".*" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
258 <param name="manipulation_type_selector" value="identifier" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
259 <param name="manipulation_selector" value="translate" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
260 <param name="from" value="" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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261 <param name="to" value="" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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262 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
263 </test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
264 <!-- match None and do nothing --> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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265 <test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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266 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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267 <param name="match_type_selector" value="identifier" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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268 <param name="match_selector" value="regex" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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269 <param name="match_by" value="STRINGDOESNOTEXIST" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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270 <param name="manipulation_type_selector" value="identifier" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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271 <param name="manipulation_selector" value="translate" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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272 <param name="from" value="" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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273 <param name="to" value="" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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274 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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275 </test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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276 <!-- match all and remove --> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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277 <test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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278 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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279 <param name="match_type_selector" value="identifier" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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280 <param name="match_selector" value="regex" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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281 <param name="match_by" value=".*" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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282 <param name="manipulation_type_selector" value="miscellaneous" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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283 <param name="manipulation_selector" value="remove" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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284 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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285 </test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
286 <!-- match None and remove --> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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287 <test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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288 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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289 <param name="match_type_selector" value="identifier" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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290 <param name="match_selector" value="regex" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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291 <param name="match_by" value="STRINGDOESNOTEXIST" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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292 <param name="manipulation_type_selector" value="miscellaneous" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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293 <param name="manipulation_selector" value="remove" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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294 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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|
295 </test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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296 <!-- match all and trim to 4 inner-most bases --> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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297 <test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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298 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
299 <param name="match_type_selector" value="identifier" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
300 <param name="match_selector" value="regex" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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301 <param name="match_by" value=".*" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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302 <param name="manipulation_type_selector" value="sequence" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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303 <param name="manipulation_selector" value="trim" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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304 <param name="base_offset_type" value="offsets_absolute"/> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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305 <param name="left_column_offset" value="45"/> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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306 <param name="right_column_offset" value="45"/> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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307 <param name="keep_zero_length" value="true" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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308 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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309 </test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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310 <test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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311 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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312 <param name="match_type_selector" value="identifier" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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313 <param name="match_selector" value="regex" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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314 <param name="match_by" value=".*" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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315 <param name="manipulation_type_selector" value="sequence" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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316 <param name="manipulation_selector" value="trim" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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317 <param name="base_offset_type" value="offsets_percent"/> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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318 <param name="left_column_offset" value="47.87"/> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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319 <param name="right_column_offset" value="47.87"/> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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320 <param name="keep_zero_length" value="true" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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321 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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322 </test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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323 <!-- match all and rev comp --> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
324 <test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
325 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
326 <param name="match_type_selector" value="identifier" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
327 <param name="match_selector" value="regex" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
328 <param name="match_by" value=".*" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
329 <param name="manipulation_type_selector" value="sequence" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
330 <param name="manipulation_selector" value="rev_comp" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
331 <output name="output_file" file="sanger_full_range_rev_comp.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
332 </test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
333 <!-- match all and rev comp, with ambiguous DNA --> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
334 <test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
335 <param name="input_file" value="misc_dna_original_sanger.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
336 <param name="match_type_selector" value="identifier" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
337 <param name="match_selector" value="regex" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
338 <param name="match_by" value=".*" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
339 <param name="manipulation_type_selector" value="sequence" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
340 <param name="manipulation_selector" value="rev_comp" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
341 <output name="output_file" file="misc_dna_as_sanger_rev_comp_1.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
342 </test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
343 <!-- match all and rev comp, with ambiguous RNA --> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
344 <test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
345 <param name="input_file" value="misc_rna_original_sanger.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
346 <param name="match_type_selector" value="identifier" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
347 <param name="match_selector" value="regex" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
348 <param name="match_by" value=".*" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
349 <param name="manipulation_type_selector" value="sequence" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
350 <param name="manipulation_selector" value="rev_comp" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
351 <output name="output_file" file="misc_rna_as_sanger_rev_comp_1.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
352 </test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
353 <!-- match first seq and rev comp --> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
354 <test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
355 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
356 <param name="match_type_selector" value="identifier" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
357 <param name="match_selector" value="regex" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
358 <param name="match_by" value="FAKE0001" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
359 <param name="manipulation_type_selector" value="sequence" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
360 <param name="manipulation_selector" value="rev_comp" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
361 <output name="output_file" file="sanger_full_range_rev_comp_1_seq.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
362 </test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
363 <!-- match first seq and rev comp: i.e. undo above --> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
364 <test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
365 <param name="input_file" value="sanger_full_range_rev_comp_1_seq.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
366 <param name="match_type_selector" value="identifier" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
367 <param name="match_selector" value="regex" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
368 <param name="match_by" value="FAKE0001" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
369 <param name="manipulation_type_selector" value="sequence" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
370 <param name="manipulation_selector" value="rev_comp" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
371 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
372 </test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
373 <!-- match all and DNA to RNA --> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
374 <test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
375 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
376 <param name="match_type_selector" value="identifier" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
377 <param name="match_selector" value="regex" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
378 <param name="match_by" value=".*" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
379 <param name="manipulation_type_selector" value="sequence" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
380 <param name="manipulation_selector" value="dna_to_rna" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
381 <output name="output_file" file="sanger_full_range_as_rna.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
382 </test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
383 <!-- match all and RNA to DNA--> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
384 <test> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
385 <param name="input_file" value="sanger_full_range_as_rna.fastqsanger" ftype="fastqsanger" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
386 <param name="match_type_selector" value="identifier" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
387 <param name="match_selector" value="regex" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
388 <param name="match_by" value=".*" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
389 <param name="manipulation_type_selector" value="sequence" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
changeset
|
390 <param name="manipulation_selector" value="rna_to_dna" /> |
7ea141c4c834
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
2
diff
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391 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
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392 </test> |
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393 <!-- match all and RNA to DNA (gz compressed) --> |
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394 <test> |
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395 <param name="input_file" value="sanger_full_range_as_rna.fastqsanger.gz" ftype="fastqsanger.gz" /> |
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396 <param name="match_type_selector" value="identifier" /> |
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397 <param name="match_selector" value="regex" /> |
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398 <param name="match_by" value=".*" /> |
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399 <param name="manipulation_type_selector" value="sequence" /> |
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400 <param name="manipulation_selector" value="rna_to_dna" /> |
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401 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger.gz" decompress="true" /> |
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402 </test> |
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403 <!-- match all and RNA to DNA (bz2 compressed) --> |
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404 <test> |
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405 <param name="input_file" value="sanger_full_range_as_rna.fastqsanger.bz2" ftype="fastqsanger.bz2" /> |
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406 <param name="match_type_selector" value="identifier" /> |
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407 <param name="match_selector" value="regex" /> |
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408 <param name="match_by" value=".*" /> |
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409 <param name="manipulation_type_selector" value="sequence" /> |
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410 <param name="manipulation_selector" value="rna_to_dna" /> |
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411 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger.bz2" decompress="true" /> |
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412 </test> |
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413 </tests> |
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414 <help><![CDATA[ |
0 | 415 This tool allows you to build complex manipulations to be applied to each matching read in a FASTQ file. A read must match all matching directives in order for it to be manipulated; if a read does not match, it is output in a non-modified manner. All reads matching will have each of the specified manipulations performed upon them, in the order specified. |
416 | |
417 Regular Expression Matches are made using re.search, see http://docs.python.org/library/re.html for more information. | |
418 All matching is performed on a single line string, regardless if e.g. the sequence or quality score spans multiple lines in the original file. | |
419 | |
420 String translations are performed using string.translate, see http://docs.python.org/library/string.html#string.translate and http://docs.python.org/library/string.html#string.maketrans for more information. | |
421 | |
422 .. class:: warningmark | |
423 | |
424 Only color space reads can have adapter bases substituted. | |
425 | |
426 ----- | |
427 | |
428 **Example** | |
429 | |
430 Suppose you have a color space sanger formatted sequence (fastqcssanger) and you want to double-encode the color space into psuedo-nucleotide space (this is different from converting) to allow these reads to be used in tools which do not natively support it (using specially designed indexes). This tool can handle this manipulation, however, this is generally not recommended as results tend to be poorer than those produced from tools which are specially designed to handle color space data. | |
431 | |
432 Steps: | |
433 | |
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434 1. Click **Add new Match Reads** and leave the matching options set to the default (Matching by sequence name/identifier using the regular expression "\*."; thereby matching all reads). |
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435 2. Click **Add new Manipulate Reads**, change **Manipulate Reads on** to "Sequence Content", set **Sequence Manipulation Type** to "Change Adapter Base" and set **New Adapter** to "" (an empty text field). |
0 | 436 3. Click **Add new Manipulate Reads**, change **Manipulate Reads on** to "Sequence Content", set **Sequence Manipulation Type** to "String Translate" and set **From** to "0123." and **To** to "ACGTN". |
437 4. Click Execute. The new history item will contained double-encoded psuedo-nucleotide space reads. | |
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438 ]]></help> |
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439 <citations> |
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440 <citation type="doi">10.1093/bioinformatics/btq281</citation> |
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441 </citations> |
0 | 442 </tool> |