fastq_manipulation: fastq_manipulation.xml annotate

annotate fastq_manipulation.xml @ 2:4ac14b275aca draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a

author	devteam
date	Sat, 30 Sep 2017 14:58:21 -0400
parents	bb07615a5b6a
children	7861f3b10c68

rev	line source
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	1 <tool id="fastq_manipulation" name="Manipulate FASTQ" version="1.1.1">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	2 <options sanitize="false" /> <!-- This tool uses a file to rely all parameter information (actually a dynamically generated python module), we can safely not sanitize any parameters -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	3 <description>reads on various attributes</description>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	4 <requirements>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	5 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	6 </requirements>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	7 <command><![CDATA[
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	8 gx-fastq-manipulation '$input_file' '$fastq_manipulation_file' '$output_file' '$output_file.files_path' '${input_file.extension[len('fastq'):]}'
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	9 ]]></command>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	10 <configfiles>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	11 <configfile name="fastq_manipulation_file"><![CDATA[##create an importable module
0 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	12 #import binascii
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	13 import binascii
0 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	14 import re
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	15 import six
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	16
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	17 if six.PY2:
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	18 from string import maketrans
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	19 else:
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	20 maketrans = str.maketrans
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	21
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	22
0 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	23 ##does read match
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	24 def match_read(fastq_read):
0 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	25 #for $match_block in $match_blocks:
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	26 #if $match_block['match_type']['match_type_selector'] == 'identifier':
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	27 search_target = fastq_read.identifier[1:] ##don't include @
0 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	28 #elif $match_block['match_type']['match_type_selector'] == 'sequence':
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	29 search_target = fastq_read.sequence
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	30 #elif $match_block['match_type']['match_type_selector'] == 'quality':
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	31 search_target = fastq_read.quality
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	32 #else:
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	33 #continue
0 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	34 #end if
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	35 if not re.search(binascii.unhexlify("${ binascii.hexlify(str(match_block['match_type']['match']['match_by'])) }").decode(), search_target):
0 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	36 return False
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	37 #end for
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	38 return True
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	39
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	40
0 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	41 ##modify matched reads
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	42 def manipulate_read(fastq_read):
0 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	43 new_read = fastq_read.clone()
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	44 #for $manipulate_block in $manipulate_blocks:
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	45 #if $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'identifier':
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	46 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'translate':
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	47 new_read.identifier = "@%s" % new_read.identifier[1:].translate(maketrans(binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from'])) }").decode(), binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to'])) }").decode()))
0 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	48 #end if
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	49 #elif $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'sequence':
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	50 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'translate':
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	51 new_read.sequence = new_read.sequence.translate(maketrans(binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from'])) }").decode(), binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to'])) }").decode()))
0 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	52 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'rev_comp':
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	53 new_read = new_read.reverse_complement()
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	54 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'rev_no_comp':
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	55 new_read = new_read.reverse()
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	56 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'no_rev_comp':
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	57 new_read = new_read.complement()
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	58 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'trim':
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	59 #if $manipulate_block['manipulation_type']['manipulation']['offset_type']['base_offset_type'] == 'offsets_percent':
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	60 left_column_offset = int(round(float(${ manipulate_block['manipulation_type']['manipulation']['offset_type']['left_column_offset'] }) / 100.0 * float(len(new_read))))
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	61 right_column_offset = int(round(float(${ manipulate_block['manipulation_type']['manipulation']['offset_type']['right_column_offset'] }) / 100.0 * float(len(new_read))))
0 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	62 #else
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	63 left_column_offset = ${ manipulate_block['manipulation_type']['manipulation']['offset_type']['left_column_offset'] }
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	64 right_column_offset = ${ manipulate_block['manipulation_type']['manipulation']['offset_type']['right_column_offset'] }
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	65 #end if
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	66 if right_column_offset != 0:
0 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	67 right_column_offset = -right_column_offset
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	68 else:
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	69 right_column_offset = None
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	70 new_read = new_read.slice(left_column_offset, right_column_offset)
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	71 if not (${str(manipulate_block['manipulation_type']['manipulation']['keep_zero_length']) == 'keep_zero_length'} or len(new_read)):
0 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	72 return None
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	73 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'dna_to_rna':
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	74 new_read = new_read.sequence_as_DNA()
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	75 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'rna_to_dna':
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	76 new_read = new_read.sequence_as_RNA()
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	77 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'change_adapter':
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	78 if new_read.sequence_space == 'color':
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	79 new_read = new_read.change_adapter(binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['new_adapter'])) }").decode())
0 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	80 #end if
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	81 #elif $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'quality':
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	82 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'translate':
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	83 new_read.quality = new_read.quality.translate(maketrans(binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from'])) }").decode(), binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to'])) }").decode()))
0 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	84 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'map_score':
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	85 def score_method(score):
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	86 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
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	87 new_read.quality_map(score_method)
0 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	88 #end if
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	89 #elif $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'miscellaneous':
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	90 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'remove':
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	91 return None
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	92 #end if
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	93 #else:
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	94 #continue
0 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	95 #end if
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	96 #end for
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	97 if new_read.description != "+":
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	98 new_read.description = "+%s" % new_read.identifier[1:] ##ensure description is still valid
0 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	99 return new_read
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	100
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	101
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	102 def match_and_manipulate_read(fastq_read):
0 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	103 new_read = fastq_read
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	104 if match_read(fastq_read):
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	105 new_read = manipulate_read(fastq_read)
0 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	106 return new_read
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	107 ]]></configfile>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	108 </configfiles>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	109 <inputs>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	110 <!-- This tool is purposely over-engineered (e.g. Single option conditionals) to allow easy enhancement with workflow/rerun compatibility -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	111 <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"/>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	112 <!-- Match Reads -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	113 <repeat name="match_blocks" title="Match Reads">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	114 <conditional name="match_type">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	115 <param name="match_type_selector" type="select" label="Match Reads by">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	116 <option value="identifier">Name/Identifier</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	117 <option value="sequence">Sequence Content</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	118 <option value="quality">Quality Score Content</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	119 </param>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	120 <when value="identifier">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	121 <conditional name="match">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	122 <param name="match_selector" type="select" label="Identifier Match Type">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	123 <option value="regex">Regular Expression</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	124 </param>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	125 <when value="regex">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	126 <param name="match_by" type="text" value=".*" label="Match by" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	127 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	128 </conditional>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	129 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	130 <when value="sequence">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	131 <conditional name="match">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	132 <param name="match_selector" type="select" label="Sequence Match Type">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	133 <option value="regex">Regular Expression</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	134 </param>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	135 <when value="regex">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	136 <param name="match_by" type="text" value=".*" label="Match by" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	137 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	138 </conditional>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	139 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	140 <when value="quality">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	141 <conditional name="match">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	142 <param name="match_selector" type="select" label="Quality Match Type">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	143 <option value="regex">Regular Expression</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	144 </param>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	145 <when value="regex">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	146 <param name="match_by" type="text" value=".*" label="Match by" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	147 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	148 </conditional>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	149 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	150 </conditional>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	151 </repeat>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	152 <!-- Manipulate Matched Reads -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	153 <repeat name="manipulate_blocks" title="Manipulate Reads">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	154 <conditional name="manipulation_type">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	155 <param name="manipulation_type_selector" type="select" label="Manipulate Reads on">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	156 <option value="identifier">Name/Identifier</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	157 <option value="sequence">Sequence Content</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	158 <option value="quality">Quality Score Content</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	159 <option value="miscellaneous">Miscellaneous Actions</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	160 </param>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	161 <when value="identifier">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	162 <conditional name="manipulation">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	163 <param name="manipulation_selector" type="select" label="Identifier Manipulation Type">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	164 <option value="translate">String Translate</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	165 </param>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	166 <when value="translate">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	167 <param name="from" type="text" value="" label="From" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	168 <param name="to" type="text" value="" label="To" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	169 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	170 </conditional>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	171 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	172 <when value="sequence">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	173 <conditional name="manipulation">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	174 <param name="manipulation_selector" type="select" label="Sequence Manipulation Type">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	175 <option value="rev_comp">Reverse Complement</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	176 <option value="rev_no_comp">Reverse, No Complement</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	177 <option value="no_rev_comp">Complement, No Reverse</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	178 <option value="trim">Trim</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	179 <option value="dna_to_rna">DNA to RNA</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	180 <option value="rna_to_dna">RNA to DNA</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	181 <option value="translate">String Translate</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	182 <option value="change_adapter">Change Adapter Base</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	183 </param>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	184 <when value="rev_comp" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	185 <when value="rev_no_comp" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	186 <when value="no_rev_comp" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	187 <when value="trim">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	188 <conditional name="offset_type">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	189 <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)">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	190 <option value="offsets_absolute" selected="true">Absolute Values</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	191 <option value="offsets_percent">Percentage of Read Length</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	192 </param>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	193 <when value="offsets_absolute">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	194 <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" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	195 <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" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	196 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	197 <when value="offsets_percent">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	198 <param name="left_column_offset" type="float" min="0" max="100" value="0" label="Offset from 5' end" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	199 <param name="right_column_offset" type="float" min="0" max="100" value="0" label="Offset from 3' end" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	200 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	201 </conditional>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	202 <param name="keep_zero_length" type="boolean" truevalue="keep_zero_length" falsevalue="exclude_zero_length" checked="false" label="Keep reads with zero length" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	203 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	204 <when value="dna_to_rna" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	205 <when value="rna_to_dna" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	206 <when value="translate">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	207 <param name="from" type="text" value="" label="From" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	208 <param name="to" type="text" value="" label="To" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	209 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	210 <when value="change_adapter">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	211 <param name="new_adapter" type="text" value="G" label="New adapter" help="An empty string will remove the adapter base" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	212 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	213 </conditional>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	214 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	215 <when value="quality">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	216 <conditional name="manipulation">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	217 <param name="manipulation_selector" type="select" label="Quality Manipulation Type">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	218 <option value="translate">String Translate</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	219 <!-- <option value="modify_each_score">Apply Transformation to each Score</option> Not enabled yet-->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	220 </param>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	221 <when value="translate">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	222 <param name="from" type="text" value="" label="From" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	223 <param name="to" type="text" value="" label="To" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	224 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	225 <!-- <when value="modify_each_score">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	226 <param name="map_score" type="text" label="Modify Score by" value="$score + 1" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	227 </when> -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	228 </conditional>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	229 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	230 <when value="miscellaneous">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	231 <conditional name="manipulation">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	232 <param name="manipulation_selector" type="select" label="Miscellaneous Manipulation Type">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	233 <option value="remove">Remove Read</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	234 </param>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	235 <when value="remove" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	236 </conditional>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	237 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	238 </conditional>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	239 </repeat>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	240 </inputs>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	241 <outputs>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	242 <data name="output_file" format_source="input_file" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	243 </outputs>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	244 <tests>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	245 <!-- match all and do nothing -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	246 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	247 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	248 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	249 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	250 <param name="match_by" value=".*" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	251 <param name="manipulation_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	252 <param name="manipulation_selector" value="translate" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	253 <param name="from" value="" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	254 <param name="to" value="" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	255 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	256 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	257 <!-- match None and do nothing -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	258 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	259 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	260 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	261 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	262 <param name="match_by" value="STRINGDOESNOTEXIST" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	263 <param name="manipulation_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	264 <param name="manipulation_selector" value="translate" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	265 <param name="from" value="" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	266 <param name="to" value="" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	267 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	268 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	269 <!-- match all and remove -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	270 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	271 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	272 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	273 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	274 <param name="match_by" value=".*" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	275 <param name="manipulation_type_selector" value="miscellaneous" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	276 <param name="manipulation_selector" value="remove" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	277 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	278 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	279 <!-- match None and remove -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	280 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	281 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	282 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	283 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	284 <param name="match_by" value="STRINGDOESNOTEXIST" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	285 <param name="manipulation_type_selector" value="miscellaneous" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	286 <param name="manipulation_selector" value="remove" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	287 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	288 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	289 <!-- match all and trim to 4 inner-most bases -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	290 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	291 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	292 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	293 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	294 <param name="match_by" value=".*" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	295 <param name="manipulation_type_selector" value="sequence" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	296 <param name="manipulation_selector" value="trim" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	297 <param name="base_offset_type" value="offsets_absolute"/>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	298 <param name="left_column_offset" value="45"/>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	299 <param name="right_column_offset" value="45"/>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	300 <param name="keep_zero_length" value="true" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	301 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	302 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	303 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	304 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	305 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	306 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	307 <param name="match_by" value=".*" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	308 <param name="manipulation_type_selector" value="sequence" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	309 <param name="manipulation_selector" value="trim" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	310 <param name="base_offset_type" value="offsets_percent"/>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	311 <param name="left_column_offset" value="47.87"/>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	312 <param name="right_column_offset" value="47.87"/>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	313 <param name="keep_zero_length" value="true" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	314 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	315 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	316 <!-- match all and rev comp -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	317 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	318 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	319 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	320 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	321 <param name="match_by" value=".*" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	322 <param name="manipulation_type_selector" value="sequence" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	323 <param name="manipulation_selector" value="rev_comp" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	324 <output name="output_file" file="sanger_full_range_rev_comp.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	325 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	326 <!-- match all and rev comp, with ambiguous DNA -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	327 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	328 <param name="input_file" value="misc_dna_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	329 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	330 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	331 <param name="match_by" value=".*" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	332 <param name="manipulation_type_selector" value="sequence" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	333 <param name="manipulation_selector" value="rev_comp" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	334 <output name="output_file" file="misc_dna_as_sanger_rev_comp_1.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	335 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	336 <!-- match all and rev comp, with ambiguous RNA -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	337 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	338 <param name="input_file" value="misc_rna_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	339 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	340 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	341 <param name="match_by" value=".*" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	342 <param name="manipulation_type_selector" value="sequence" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	343 <param name="manipulation_selector" value="rev_comp" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	344 <output name="output_file" file="misc_rna_as_sanger_rev_comp_1.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	345 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	346 <!-- match first seq and rev comp -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	347 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	348 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	349 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	350 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	351 <param name="match_by" value="FAKE0001" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	352 <param name="manipulation_type_selector" value="sequence" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	353 <param name="manipulation_selector" value="rev_comp" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	354 <output name="output_file" file="sanger_full_range_rev_comp_1_seq.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	355 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	356 <!-- match first seq and rev comp: i.e. undo above -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	357 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	358 <param name="input_file" value="sanger_full_range_rev_comp_1_seq.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	359 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	360 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	361 <param name="match_by" value="FAKE0001" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	362 <param name="manipulation_type_selector" value="sequence" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	363 <param name="manipulation_selector" value="rev_comp" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	364 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	365 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	366 <!-- match all and DNA to RNA -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	367 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	368 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	369 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	370 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	371 <param name="match_by" value=".*" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	372 <param name="manipulation_type_selector" value="sequence" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	373 <param name="manipulation_selector" value="dna_to_rna" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	374 <output name="output_file" file="sanger_full_range_as_rna.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	375 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	376 <!-- match all and RNA to DNA-->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	377 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	378 <param name="input_file" value="sanger_full_range_as_rna.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	379 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	380 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	381 <param name="match_by" value=".*" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	382 <param name="manipulation_type_selector" value="sequence" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	383 <param name="manipulation_selector" value="rna_to_dna" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	384 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	385 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	386 <!-- match all and RNA to DNA (gz compressed) -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	387 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	388 <param name="input_file" value="sanger_full_range_as_rna.fastqsanger.gz" ftype="fastqsanger.gz" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	389 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	390 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	391 <param name="match_by" value=".*" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	392 <param name="manipulation_type_selector" value="sequence" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	393 <param name="manipulation_selector" value="rna_to_dna" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	394 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	395 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	396 <!-- match all and RNA to DNA (bz2 compressed) -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	397 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	398 <param name="input_file" value="sanger_full_range_as_rna.fastqsanger.bz2" ftype="fastqsanger.bz2" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	399 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	400 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	401 <param name="match_by" value=".*" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	402 <param name="manipulation_type_selector" value="sequence" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	403 <param name="manipulation_selector" value="rna_to_dna" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	404 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	405 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	406 </tests>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	407 <help><![CDATA[
0 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	408 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.
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	409
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	410 Regular Expression Matches are made using re.search, see http://docs.python.org/library/re.html for more information.
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	411 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.
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	412
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	413 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.
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	414
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	415 .. class:: warningmark
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	416
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	417 Only color space reads can have adapter bases substituted.
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	418
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	419 -----
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	420
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	421 Example
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	422
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	423 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.
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	424
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	425 Steps:
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	426
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	427 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).
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	428 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 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	429 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".
5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	430 4. Click Execute. The new history item will contained double-encoded psuedo-nucleotide space reads.
2 4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	431 ]]></help>
1 bb07615a5b6a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a1517c9d22029095120643bbe2c8fa53754dd2b7 devteam parents: 0 diff changeset	432 <citations>
bb07615a5b6a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a1517c9d22029095120643bbe2c8fa53754dd2b7 devteam parents: 0 diff changeset	433 <citation type="doi">10.1093/bioinformatics/btq281</citation>
bb07615a5b6a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a1517c9d22029095120643bbe2c8fa53754dd2b7 devteam parents: 0 diff changeset	434 </citations>
0 5d1e9e13e8db Imported from capsule None devteam parents: diff changeset	435 </tool>

Mercurial > repos > devteam > fastq_manipulation

annotate fastq_manipulation.xml @ 2:4ac14b275aca draft