fastq_manipulation: fastq_manipulation.xml annotate

annotate fastq_manipulation.xml @ 6:ed6c5df75175 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845

author	iuc
date	Fri, 04 Oct 2024 10:33:21 +0000
parents	b77ecfa1664e
children

rev	line source
6 ed6c5df75175 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845 iuc parents: 5 diff changeset	1 <tool id="fastq_manipulation" name="Manipulate FASTQ" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
4 6f864b826b3e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit 31edb920789fbd080260f853bc856be72fa7cfa8" devteam parents: 3 diff changeset	2 <!-- This tool uses a file to rely all parameter information (actually a dynamically generated python module), we can safely not sanitize any parameters -->
3 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	3 <description>reads on various attributes</description>
5 b77ecfa1664e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit d4ced60a941c4c4a2fe95de9c09a10086810b387" iuc parents: 4 diff changeset	4 <macros>
b77ecfa1664e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit d4ced60a941c4c4a2fe95de9c09a10086810b387" iuc parents: 4 diff changeset	5 <import>macros.xml</import>
b77ecfa1664e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit d4ced60a941c4c4a2fe95de9c09a10086810b387" iuc parents: 4 diff changeset	6 </macros>
6 ed6c5df75175 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845 iuc parents: 5 diff changeset	7 <options sanitize="false" />
4 6f864b826b3e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit 31edb920789fbd080260f853bc856be72fa7cfa8" devteam parents: 3 diff changeset	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" devteam parents: 3 diff changeset	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" devteam parents: 3 diff changeset	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" devteam parents: 3 diff changeset	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" devteam parents: 3 diff changeset	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" devteam parents: 3 diff changeset	13 </edam_operations>
6 ed6c5df75175 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845 iuc parents: 5 diff changeset	14 <expand macro="requirements"/>
3 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	15 <command><![CDATA[
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	16 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 devteam parents: 2 diff changeset	17 ]]></command>
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	18 <configfiles>
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	19 <configfile name="fastq_manipulation_file"><![CDATA[##create an importable module
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	20 #import binascii
3 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	21 import binascii
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	22 import re
3 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	23 import six
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	24
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	25 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 devteam parents: 2 diff changeset	26 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 devteam parents: 2 diff changeset	27 else:
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	28 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 devteam parents: 2 diff changeset	29
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	30
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	31 ##does read match
3 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	32 def match_read(fastq_read):
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	33 #for $match_block in $match_blocks:
de14b969d713 Imported from capsule None devteam parents: diff changeset	34 #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 devteam parents: 2 diff changeset	35 search_target = fastq_read.identifier[1:] ##don't include @
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	36 #elif $match_block['match_type']['match_type_selector'] == 'sequence':
de14b969d713 Imported from capsule None devteam parents: diff changeset	37 search_target = fastq_read.sequence
de14b969d713 Imported from capsule None devteam parents: diff changeset	38 #elif $match_block['match_type']['match_type_selector'] == 'quality':
de14b969d713 Imported from capsule None devteam parents: diff changeset	39 search_target = fastq_read.quality
de14b969d713 Imported from capsule None devteam parents: diff changeset	40 #else:
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	41 #continue
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	42 #end if
5 b77ecfa1664e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit d4ced60a941c4c4a2fe95de9c09a10086810b387" iuc parents: 4 diff changeset	43 if not re.search(binascii.unhexlify(${ binascii.hexlify(str(match_block['match_type']['match']['match_by']).encode()) }).decode(), search_target):
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	44 return False
de14b969d713 Imported from capsule None devteam parents: diff changeset	45 #end for
de14b969d713 Imported from capsule None devteam parents: diff changeset	46 return True
3 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	47
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	48
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	49 ##modify matched reads
3 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	50 def manipulate_read(fastq_read):
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	51 new_read = fastq_read.clone()
de14b969d713 Imported from capsule None devteam parents: diff changeset	52 #for $manipulate_block in $manipulate_blocks:
de14b969d713 Imported from capsule None devteam parents: diff changeset	53 #if $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'identifier':
de14b969d713 Imported from capsule None devteam parents: diff changeset	54 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'translate':
5 b77ecfa1664e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit d4ced60a941c4c4a2fe95de9c09a10086810b387" iuc parents: 4 diff changeset	55 new_read.identifier = "@%s" % new_read.identifier[1:].translate(maketrans(binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from']).encode()) }).decode(), binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to']).encode()) }).decode()))
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	56 #end if
de14b969d713 Imported from capsule None devteam parents: diff changeset	57 #elif $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'sequence':
de14b969d713 Imported from capsule None devteam parents: diff changeset	58 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'translate':
5 b77ecfa1664e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit d4ced60a941c4c4a2fe95de9c09a10086810b387" iuc parents: 4 diff changeset	59 new_read.sequence = new_read.sequence.translate(maketrans(binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from']).encode()) }).decode(), binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to']).encode()) }).decode()))
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	60 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'rev_comp':
de14b969d713 Imported from capsule None devteam parents: diff changeset	61 new_read = new_read.reverse_complement()
de14b969d713 Imported from capsule None devteam parents: diff changeset	62 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'rev_no_comp':
de14b969d713 Imported from capsule None devteam parents: diff changeset	63 new_read = new_read.reverse()
de14b969d713 Imported from capsule None devteam parents: diff changeset	64 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'no_rev_comp':
de14b969d713 Imported from capsule None devteam parents: diff changeset	65 new_read = new_read.complement()
de14b969d713 Imported from capsule None devteam parents: diff changeset	66 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'trim':
de14b969d713 Imported from capsule None devteam parents: diff changeset	67 #if $manipulate_block['manipulation_type']['manipulation']['offset_type']['base_offset_type'] == 'offsets_percent':
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	68 left_column_offset = int(round(float(${ 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 devteam parents: 2 diff changeset	69 right_column_offset = int(round(float(${ manipulate_block['manipulation_type']['manipulation']['offset_type']['right_column_offset'] }) / 100.0 * float(len(new_read))))
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	70 #else
de14b969d713 Imported from capsule None devteam parents: diff changeset	71 left_column_offset = ${ manipulate_block['manipulation_type']['manipulation']['offset_type']['left_column_offset'] }
de14b969d713 Imported from capsule None devteam parents: diff changeset	72 right_column_offset = ${ manipulate_block['manipulation_type']['manipulation']['offset_type']['right_column_offset'] }
de14b969d713 Imported from capsule None devteam parents: diff changeset	73 #end if
2 16d28d67ebeb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit de7140295cce07e1bc1697e51dab4271c8d7a8a6 devteam parents: 1 diff changeset	74 if right_column_offset != 0:
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	75 right_column_offset = -right_column_offset
de14b969d713 Imported from capsule None devteam parents: diff changeset	76 else:
de14b969d713 Imported from capsule None devteam parents: diff changeset	77 right_column_offset = None
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	78 new_read = new_read.slice(left_column_offset, right_column_offset)
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	79 if not (${str(manipulate_block['manipulation_type']['manipulation']['keep_zero_length']) == 'keep_zero_length'} or len(new_read)):
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	80 return None
de14b969d713 Imported from capsule None devteam parents: diff changeset	81 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'dna_to_rna':
de14b969d713 Imported from capsule None devteam parents: diff changeset	82 new_read = new_read.sequence_as_DNA()
de14b969d713 Imported from capsule None devteam parents: diff changeset	83 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'rna_to_dna':
de14b969d713 Imported from capsule None devteam parents: diff changeset	84 new_read = new_read.sequence_as_RNA()
de14b969d713 Imported from capsule None devteam parents: diff changeset	85 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'change_adapter':
de14b969d713 Imported from capsule None devteam parents: diff changeset	86 if new_read.sequence_space == 'color':
5 b77ecfa1664e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit d4ced60a941c4c4a2fe95de9c09a10086810b387" iuc parents: 4 diff changeset	87 new_read = new_read.change_adapter(binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['new_adapter']).encode()) }).decode())
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	88 #end if
de14b969d713 Imported from capsule None devteam parents: diff changeset	89 #elif $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'quality':
de14b969d713 Imported from capsule None devteam parents: diff changeset	90 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'translate':
5 b77ecfa1664e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit d4ced60a941c4c4a2fe95de9c09a10086810b387" iuc parents: 4 diff changeset	91 new_read.quality = new_read.quality.translate(maketrans(binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from'])).encode() }).decode(), binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to']).encode()) }).decode()))
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	92 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'map_score':
3 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	93 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 devteam parents: 2 diff changeset	94 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 devteam parents: 2 diff changeset	95 new_read.quality_map(score_method)
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	96 #end if
de14b969d713 Imported from capsule None devteam parents: diff changeset	97 #elif $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'miscellaneous':
de14b969d713 Imported from capsule None devteam parents: diff changeset	98 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'remove':
de14b969d713 Imported from capsule None devteam parents: diff changeset	99 return None
de14b969d713 Imported from capsule None devteam parents: diff changeset	100 #end if
de14b969d713 Imported from capsule None devteam parents: diff changeset	101 #else:
3 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	102 #continue
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	103 #end if
de14b969d713 Imported from capsule None devteam parents: diff changeset	104 #end for
de14b969d713 Imported from capsule None devteam parents: diff changeset	105 if new_read.description != "+":
3 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	106 new_read.description = "+%s" % new_read.identifier[1:] ##ensure description is still valid
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	107 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 devteam parents: 2 diff changeset	108
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	109
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	110 def match_and_manipulate_read(fastq_read):
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	111 new_read = fastq_read
3 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	112 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 devteam parents: 2 diff changeset	113 new_read = manipulate_read(fastq_read)
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	114 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 devteam parents: 2 diff changeset	115 ]]></configfile>
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	116 </configfiles>
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	117 <inputs>
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	118 <!-- 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 devteam parents: 2 diff changeset	119 <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 devteam parents: 2 diff changeset	120 <!-- Match Reads -->
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	121 <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 devteam parents: 2 diff changeset	122 <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 devteam parents: 2 diff changeset	123 <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: 2 diff changeset	124 <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 devteam parents: 2 diff changeset	125 <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 devteam parents: 2 diff changeset	126 <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 devteam parents: 2 diff changeset	127 </param>
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	128 <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 devteam parents: 2 diff changeset	129 <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 devteam parents: 2 diff changeset	130 <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 devteam parents: 2 diff changeset	131 <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 devteam parents: 2 diff changeset	132 </param>
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	133 <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 devteam parents: 2 diff changeset	134 <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 devteam parents: 2 diff changeset	135 </when>
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	136 </conditional>
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	137 </when>
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	138 <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 devteam parents: 2 diff changeset	139 <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 devteam parents: 2 diff changeset	140 <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 devteam parents: 2 diff changeset	141 <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 devteam parents: 2 diff changeset	142 </param>
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	143 <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 devteam parents: 2 diff changeset	144 <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 devteam parents: 2 diff changeset	145 </when>
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	146 </conditional>
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	147 </when>
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	148 <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 devteam parents: 2 diff changeset	149 <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 devteam parents: 2 diff changeset	150 <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 devteam parents: 2 diff changeset	151 <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 devteam parents: 2 diff changeset	152 </param>
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	153 <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 devteam parents: 2 diff changeset	154 <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 devteam parents: 2 diff changeset	155 </when>
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	156 </conditional>
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	157 </when>
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	158 </conditional>
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	159 </repeat>
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	160 <!-- 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 devteam parents: 2 diff changeset	161 <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 devteam parents: 2 diff changeset	162 <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 devteam parents: 2 diff changeset	163 <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 devteam parents: 2 diff changeset	164 <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 devteam parents: 2 diff changeset	165 <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 devteam parents: 2 diff changeset	166 <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 devteam parents: 2 diff changeset	167 <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 devteam parents: 2 diff changeset	168 </param>
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	169 <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 devteam parents: 2 diff changeset	170 <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 devteam parents: 2 diff changeset	171 <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 devteam parents: 2 diff changeset	172 <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 devteam parents: 2 diff changeset	173 </param>
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	174 <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 devteam parents: 2 diff changeset	175 <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 devteam parents: 2 diff changeset	176 <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 devteam parents: 2 diff changeset	177 </when>
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	178 </conditional>
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	179 </when>
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	180 <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 devteam parents: 2 diff changeset	181 <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 devteam parents: 2 diff changeset	182 <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 devteam parents: 2 diff changeset	183 <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 devteam parents: 2 diff changeset	184 <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 devteam parents: 2 diff changeset	185 <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 devteam parents: 2 diff changeset	186 <option value="trim">Trim</option>
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	187 <option value="dna_to_rna">DNA to RNA</option>
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	188 <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 devteam parents: 2 diff changeset	189 <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 devteam parents: 2 diff changeset	190 <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 devteam parents: 2 diff changeset	191 </param>
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	192 <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 devteam parents: 2 diff changeset	193 <when value="rev_no_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	194 <when value="no_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	195 <when value="trim">
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	196 <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 devteam parents: 2 diff changeset	197 <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 devteam parents: 2 diff changeset	198 <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 devteam parents: 2 diff changeset	199 <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 devteam parents: 2 diff changeset	200 </param>
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	201 <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 devteam parents: 2 diff changeset	202 <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 devteam parents: 2 diff changeset	203 <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 devteam parents: 2 diff changeset	204 </when>
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	205 <when 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 devteam parents: 2 diff changeset	206 <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 devteam parents: 2 diff changeset	207 <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 devteam parents: 2 diff changeset	208 </when>
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	209 </conditional>
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	210 <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 devteam parents: 2 diff changeset	211 </when>
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	212 <when 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	213 <when 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 changeset	214 <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 devteam parents: 2 diff changeset	215 <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 devteam parents: 2 diff changeset	216 <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 devteam parents: 2 diff changeset	217 </when>
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	218 <when value="change_adapter">
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	219 <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 devteam parents: 2 diff changeset	220 </when>
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	221 </conditional>
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	222 </when>
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	223 <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 devteam parents: 2 diff changeset	224 <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 devteam parents: 2 diff changeset	225 <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 devteam parents: 2 diff changeset	226 <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 devteam parents: 2 diff changeset	227 <!-- <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 devteam parents: 2 diff changeset	228 </param>
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	229 <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 devteam parents: 2 diff changeset	230 <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 devteam parents: 2 diff changeset	231 <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 devteam parents: 2 diff changeset	232 </when>
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	233 <!-- <when value="modify_each_score">
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	234 <param name="map_score" type="text" label="Modify Score by" value="$score + 1" />
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	235 </when> -->
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	236 </conditional>
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	237 </when>
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	238 <when value="miscellaneous">
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	239 <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 devteam parents: 2 diff changeset	240 <param name="manipulation_selector" type="select" label="Miscellaneous Manipulation Type">
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	241 <option value="remove">Remove Read</option>
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	242 </param>
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	243 <when value="remove" />
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	244 </conditional>
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	245 </when>
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	246 </conditional>
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	247 </repeat>
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	248 </inputs>
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	249 <outputs>
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	250 <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 devteam parents: 2 diff changeset	251 </outputs>
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	252 <tests>
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	253 <!-- match all 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 devteam parents: 2 diff changeset	254 <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	255 <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	256 <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	257 <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	258 <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	259 <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 devteam parents: 2 diff changeset	260 <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 devteam parents: 2 diff changeset	261 <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 devteam parents: 2 diff changeset	262 <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 devteam parents: 2 diff changeset	263 <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	264 </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	265 <!-- 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 devteam parents: 2 diff changeset	266 <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	267 <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	268 <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	269 <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	270 <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 devteam parents: 2 diff changeset	271 <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 devteam parents: 2 diff changeset	272 <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 devteam parents: 2 diff changeset	273 <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 devteam parents: 2 diff changeset	274 <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 devteam parents: 2 diff changeset	275 <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	276 </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	277 <!-- 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 devteam parents: 2 diff changeset	278 <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	279 <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	280 <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	281 <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	282 <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	283 <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 devteam parents: 2 diff changeset	284 <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 devteam parents: 2 diff changeset	285 <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 devteam parents: 2 diff changeset	286 </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	287 <!-- 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 devteam parents: 2 diff changeset	288 <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	289 <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	290 <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	291 <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	292 <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 devteam parents: 2 diff changeset	293 <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 devteam parents: 2 diff changeset	294 <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 devteam parents: 2 diff changeset	295 <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	296 </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	297 <!-- 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 devteam parents: 2 diff changeset	298 <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	299 <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	300 <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	301 <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	302 <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	303 <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	304 <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 devteam parents: 2 diff changeset	305 <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 devteam parents: 2 diff changeset	306 <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 devteam parents: 2 diff changeset	307 <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 devteam parents: 2 diff changeset	308 <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 devteam parents: 2 diff changeset	309 <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 devteam parents: 2 diff changeset	310 </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	311 <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	312 <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	313 <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	314 <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	315 <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	316 <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	317 <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 devteam parents: 2 diff changeset	318 <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 devteam parents: 2 diff changeset	319 <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 devteam parents: 2 diff changeset	320 <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 devteam parents: 2 diff changeset	321 <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 devteam parents: 2 diff changeset	322 <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 devteam parents: 2 diff changeset	323 </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	324 <!-- 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	325 <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	326 <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	327 <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	328 <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	329 <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	330 <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	331 <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	332 <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	333 </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	334 <!-- 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	335 <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	336 <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	337 <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	338 <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	339 <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	340 <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	341 <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	342 <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	343 </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	344 <!-- 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	345 <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	346 <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	347 <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	348 <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	349 <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	350 <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	351 <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	352 <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	353 </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	354 <!-- 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	355 <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	356 <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	357 <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	358 <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	359 <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	360 <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	361 <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	362 <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	363 </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	364 <!-- 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	365 <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	366 <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	367 <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	368 <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	369 <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	370 <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	371 <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	372 <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	373 </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	374 <!-- 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	375 <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	376 <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	377 <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	378 <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	379 <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	380 <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	381 <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	382 <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	383 </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	384 <!-- 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	385 <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	386 <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	387 <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	388 <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	389 <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	390 <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	391 <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 changeset	392 <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	393 </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	394 <!-- match all and RNA to DNA (gz compressed) -->
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	395 <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	396 <param name="input_file" value="sanger_full_range_as_rna.fastqsanger.gz" ftype="fastqsanger.gz" />
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	397 <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	398 <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	399 <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	400 <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	401 <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 changeset	402 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
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	403 </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	404 <!-- match all and RNA to DNA (bz2 compressed) -->
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	405 <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	406 <param name="input_file" value="sanger_full_range_as_rna.fastqsanger.bz2" ftype="fastqsanger.bz2" />
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	407 <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	408 <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	409 <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	410 <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	411 <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 changeset	412 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
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	413 </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	414 </tests>
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	415 <help><![CDATA[
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	416 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.
de14b969d713 Imported from capsule None devteam parents: diff changeset	417
de14b969d713 Imported from capsule None devteam parents: diff changeset	418 Regular Expression Matches are made using re.search, see http://docs.python.org/library/re.html for more information.
de14b969d713 Imported from capsule None devteam parents: diff changeset	419 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.
de14b969d713 Imported from capsule None devteam parents: diff changeset	420
de14b969d713 Imported from capsule None devteam parents: diff changeset	421 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.
de14b969d713 Imported from capsule None devteam parents: diff changeset	422
de14b969d713 Imported from capsule None devteam parents: diff changeset	423 .. class:: warningmark
de14b969d713 Imported from capsule None devteam parents: diff changeset	424
de14b969d713 Imported from capsule None devteam parents: diff changeset	425 Only color space reads can have adapter bases substituted.
de14b969d713 Imported from capsule None devteam parents: diff changeset	426
de14b969d713 Imported from capsule None devteam parents: diff changeset	427 -----
de14b969d713 Imported from capsule None devteam parents: diff changeset	428
de14b969d713 Imported from capsule None devteam parents: diff changeset	429 Example
de14b969d713 Imported from capsule None devteam parents: diff changeset	430
de14b969d713 Imported from capsule None devteam parents: diff changeset	431 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.
de14b969d713 Imported from capsule None devteam parents: diff changeset	432
de14b969d713 Imported from capsule None devteam parents: diff changeset	433 Steps:
de14b969d713 Imported from capsule None devteam parents: diff changeset	434
3 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	435 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).
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	436 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 de14b969d713 Imported from capsule None devteam parents: diff changeset	437 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".
de14b969d713 Imported from capsule None devteam parents: diff changeset	438 4. Click Execute. The new history item will contained double-encoded psuedo-nucleotide space reads.
3 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	439 ]]></help>
1 b50aeae8bcaa planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	440 <citations>
b50aeae8bcaa planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	441 <citation type="doi">10.1093/bioinformatics/btq281</citation>
b50aeae8bcaa planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	442 </citations>
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	443 </tool>

Mercurial > repos > devteam > fastq_manipulation

annotate fastq_manipulation.xml @ 6:ed6c5df75175 draft default tip