fastq_manipulation: fastq_manipulation.xml annotate

annotate fastq_manipulation.xml @ 7:3b9ecb0920bf draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9

author	iuc
date	Sun, 23 Nov 2025 17:48:47 +0000
parents	ed6c5df75175
children

rev	line source
6 ed6c5df75175 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845 iuc parents: 5 diff changeset	1 <tool id="fastq_manipulation" name="Manipulate FASTQ" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
4 6f864b826b3e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit 31edb920789fbd080260f853bc856be72fa7cfa8" devteam parents: 3 diff changeset	2 <!-- This tool uses a file to rely all parameter information (actually a dynamically generated python module), we can safely not sanitize any parameters -->
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	3 <description>reads on various attributes</description>
5 b77ecfa1664e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit d4ced60a941c4c4a2fe95de9c09a10086810b387" iuc parents: 4 diff changeset	4 <macros>
b77ecfa1664e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit d4ced60a941c4c4a2fe95de9c09a10086810b387" iuc parents: 4 diff changeset	5 <import>macros.xml</import>
b77ecfa1664e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit d4ced60a941c4c4a2fe95de9c09a10086810b387" iuc parents: 4 diff changeset	6 </macros>
6 ed6c5df75175 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845 iuc parents: 5 diff changeset	7 <options sanitize="false" />
4 6f864b826b3e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit 31edb920789fbd080260f853bc856be72fa7cfa8" devteam parents: 3 diff changeset	8 <edam_topics>
6f864b826b3e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit 31edb920789fbd080260f853bc856be72fa7cfa8" devteam parents: 3 diff changeset	9 <edam_topic>topic_0622</edam_topic>
6f864b826b3e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit 31edb920789fbd080260f853bc856be72fa7cfa8" devteam parents: 3 diff changeset	10 </edam_topics>
6f864b826b3e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit 31edb920789fbd080260f853bc856be72fa7cfa8" devteam parents: 3 diff changeset	11 <edam_operations>
6f864b826b3e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit 31edb920789fbd080260f853bc856be72fa7cfa8" devteam parents: 3 diff changeset	12 <edam_operation>operation_0233</edam_operation>
6f864b826b3e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit 31edb920789fbd080260f853bc856be72fa7cfa8" devteam parents: 3 diff changeset	13 </edam_operations>
6 ed6c5df75175 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845 iuc parents: 5 diff changeset	14 <expand macro="requirements"/>
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	15 <command><![CDATA[
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	16 gx-fastq-manipulation '$input_file' '$fastq_manipulation_file' '$output_file' '$output_file.files_path' '${input_file.extension[len('fastq'):]}'
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	17 ]]></command>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	18 <configfiles>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	19 <configfile name="fastq_manipulation_file"><![CDATA[##create an importable module
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	20 #import binascii
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	21 import binascii
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	22 import re
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	23
7 3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	24 maketrans = str.maketrans
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	25
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	26 ##does read match
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	27 def match_read(fastq_read):
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	28 #for $match_block in $match_blocks:
de14b969d713 Imported from capsule None devteam parents: diff changeset	29 #if $match_block['match_type']['match_type_selector'] == 'identifier':
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	30 search_target = fastq_read.identifier[1:] ##don't include @
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	31 #elif $match_block['match_type']['match_type_selector'] == 'sequence':
de14b969d713 Imported from capsule None devteam parents: diff changeset	32 search_target = fastq_read.sequence
de14b969d713 Imported from capsule None devteam parents: diff changeset	33 #elif $match_block['match_type']['match_type_selector'] == 'quality':
de14b969d713 Imported from capsule None devteam parents: diff changeset	34 search_target = fastq_read.quality
de14b969d713 Imported from capsule None devteam parents: diff changeset	35 #else:
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	36 #continue
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	37 #end if
5 b77ecfa1664e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit d4ced60a941c4c4a2fe95de9c09a10086810b387" iuc parents: 4 diff changeset	38 if not re.search(binascii.unhexlify(${ binascii.hexlify(str(match_block['match_type']['match']['match_by']).encode()) }).decode(), search_target):
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	39 return False
de14b969d713 Imported from capsule None devteam parents: diff changeset	40 #end for
de14b969d713 Imported from capsule None devteam parents: diff changeset	41 return True
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	42
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	43
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	44 ##modify matched reads
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	45 def manipulate_read(fastq_read):
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	46 new_read = fastq_read.clone()
de14b969d713 Imported from capsule None devteam parents: diff changeset	47 #for $manipulate_block in $manipulate_blocks:
de14b969d713 Imported from capsule None devteam parents: diff changeset	48 #if $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'identifier':
de14b969d713 Imported from capsule None devteam parents: diff changeset	49 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'translate':
5 b77ecfa1664e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit d4ced60a941c4c4a2fe95de9c09a10086810b387" iuc parents: 4 diff changeset	50 new_read.identifier = "@%s" % new_read.identifier[1:].translate(maketrans(binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from']).encode()) }).decode(), binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to']).encode()) }).decode()))
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	51 #end if
de14b969d713 Imported from capsule None devteam parents: diff changeset	52 #elif $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'sequence':
de14b969d713 Imported from capsule None devteam parents: diff changeset	53 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'translate':
5 b77ecfa1664e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit d4ced60a941c4c4a2fe95de9c09a10086810b387" iuc parents: 4 diff changeset	54 new_read.sequence = new_read.sequence.translate(maketrans(binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from']).encode()) }).decode(), binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to']).encode()) }).decode()))
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	55 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'rev_comp':
de14b969d713 Imported from capsule None devteam parents: diff changeset	56 new_read = new_read.reverse_complement()
de14b969d713 Imported from capsule None devteam parents: diff changeset	57 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'rev_no_comp':
de14b969d713 Imported from capsule None devteam parents: diff changeset	58 new_read = new_read.reverse()
de14b969d713 Imported from capsule None devteam parents: diff changeset	59 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'no_rev_comp':
de14b969d713 Imported from capsule None devteam parents: diff changeset	60 new_read = new_read.complement()
de14b969d713 Imported from capsule None devteam parents: diff changeset	61 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'trim':
de14b969d713 Imported from capsule None devteam parents: diff changeset	62 #if $manipulate_block['manipulation_type']['manipulation']['offset_type']['base_offset_type'] == 'offsets_percent':
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	63 left_column_offset = int(round(float(${ manipulate_block['manipulation_type']['manipulation']['offset_type']['left_column_offset'] }) / 100.0 * float(len(new_read))))
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	64 right_column_offset = int(round(float(${ manipulate_block['manipulation_type']['manipulation']['offset_type']['right_column_offset'] }) / 100.0 * float(len(new_read))))
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	65 #else
de14b969d713 Imported from capsule None devteam parents: diff changeset	66 left_column_offset = ${ manipulate_block['manipulation_type']['manipulation']['offset_type']['left_column_offset'] }
de14b969d713 Imported from capsule None devteam parents: diff changeset	67 right_column_offset = ${ manipulate_block['manipulation_type']['manipulation']['offset_type']['right_column_offset'] }
de14b969d713 Imported from capsule None devteam parents: diff changeset	68 #end if
2 16d28d67ebeb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit de7140295cce07e1bc1697e51dab4271c8d7a8a6 devteam parents: 1 diff changeset	69 if right_column_offset != 0:
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	70 right_column_offset = -right_column_offset
de14b969d713 Imported from capsule None devteam parents: diff changeset	71 else:
de14b969d713 Imported from capsule None devteam parents: diff changeset	72 right_column_offset = None
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	73 new_read = new_read.slice(left_column_offset, right_column_offset)
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	74 if not (${str(manipulate_block['manipulation_type']['manipulation']['keep_zero_length']) == 'keep_zero_length'} or len(new_read)):
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	75 return None
de14b969d713 Imported from capsule None devteam parents: diff changeset	76 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'dna_to_rna':
de14b969d713 Imported from capsule None devteam parents: diff changeset	77 new_read = new_read.sequence_as_DNA()
de14b969d713 Imported from capsule None devteam parents: diff changeset	78 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'rna_to_dna':
de14b969d713 Imported from capsule None devteam parents: diff changeset	79 new_read = new_read.sequence_as_RNA()
de14b969d713 Imported from capsule None devteam parents: diff changeset	80 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'change_adapter':
de14b969d713 Imported from capsule None devteam parents: diff changeset	81 if new_read.sequence_space == 'color':
5 b77ecfa1664e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit d4ced60a941c4c4a2fe95de9c09a10086810b387" iuc parents: 4 diff changeset	82 new_read = new_read.change_adapter(binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['new_adapter']).encode()) }).decode())
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	83 #end if
de14b969d713 Imported from capsule None devteam parents: diff changeset	84 #elif $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'quality':
de14b969d713 Imported from capsule None devteam parents: diff changeset	85 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'translate':
5 b77ecfa1664e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit d4ced60a941c4c4a2fe95de9c09a10086810b387" iuc parents: 4 diff changeset	86 new_read.quality = new_read.quality.translate(maketrans(binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from'])).encode() }).decode(), binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to']).encode()) }).decode()))
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	87 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'map_score':
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	88 def score_method(score):
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	89 raise Exception("Unimplemented") ##This option is not yet available, need to abstract out e.g. column adding tool action: preventing users from using 'harmful' actions
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	90 new_read.quality_map(score_method)
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	91 #end if
de14b969d713 Imported from capsule None devteam parents: diff changeset	92 #elif $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'miscellaneous':
de14b969d713 Imported from capsule None devteam parents: diff changeset	93 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'remove':
de14b969d713 Imported from capsule None devteam parents: diff changeset	94 return None
de14b969d713 Imported from capsule None devteam parents: diff changeset	95 #end if
de14b969d713 Imported from capsule None devteam parents: diff changeset	96 #else:
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	97 #continue
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	98 #end if
de14b969d713 Imported from capsule None devteam parents: diff changeset	99 #end for
de14b969d713 Imported from capsule None devteam parents: diff changeset	100 if new_read.description != "+":
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	101 new_read.description = "+%s" % new_read.identifier[1:] ##ensure description is still valid
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	102 return new_read
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	103
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	104
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	105 def match_and_manipulate_read(fastq_read):
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	106 new_read = fastq_read
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	107 if match_read(fastq_read):
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	108 new_read = manipulate_read(fastq_read)
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	109 return new_read
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	110 ]]></configfile>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	111 </configfiles>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	112 <inputs>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	113 <!-- This tool is purposely over-engineered (e.g. Single option conditionals) to allow easy enhancement with workflow/rerun compatibility -->
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	114 <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ File" help="Requires groomed data: if your data does not appear here try using the FASTQ groomer"/>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	115 <!-- Match Reads -->
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	116 <repeat name="match_blocks" title="Match Reads">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	117 <conditional name="match_type">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	118 <param name="match_type_selector" type="select" label="Match Reads by">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	119 <option value="identifier">Name/Identifier</option>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	120 <option value="sequence">Sequence Content</option>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	121 <option value="quality">Quality Score Content</option>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	122 </param>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	123 <when value="identifier">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	124 <conditional name="match">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	125 <param name="match_selector" type="select" label="Identifier Match Type">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	126 <option value="regex">Regular Expression</option>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	127 </param>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	128 <when value="regex">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	129 <param name="match_by" type="text" value=".*" label="Match by" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	130 </when>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	131 </conditional>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	132 </when>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	133 <when value="sequence">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	134 <conditional name="match">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	135 <param name="match_selector" type="select" label="Sequence Match Type">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	136 <option value="regex">Regular Expression</option>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	137 </param>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	138 <when value="regex">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	139 <param name="match_by" type="text" value=".*" label="Match by" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	140 </when>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	141 </conditional>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	142 </when>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	143 <when value="quality">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	144 <conditional name="match">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	145 <param name="match_selector" type="select" label="Quality Match Type">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	146 <option value="regex">Regular Expression</option>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	147 </param>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	148 <when value="regex">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	149 <param name="match_by" type="text" value=".*" label="Match by" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	150 </when>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	151 </conditional>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	152 </when>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	153 </conditional>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	154 </repeat>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	155 <!-- Manipulate Matched Reads -->
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	156 <repeat name="manipulate_blocks" title="Manipulate Reads">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	157 <conditional name="manipulation_type">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	158 <param name="manipulation_type_selector" type="select" label="Manipulate Reads on">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	159 <option value="identifier">Name/Identifier</option>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	160 <option value="sequence">Sequence Content</option>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	161 <option value="quality">Quality Score Content</option>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	162 <option value="miscellaneous">Miscellaneous Actions</option>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	163 </param>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	164 <when value="identifier">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	165 <conditional name="manipulation">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	166 <param name="manipulation_selector" type="select" label="Identifier Manipulation Type">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	167 <option value="translate">String Translate</option>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	168 </param>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	169 <when value="translate">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	170 <param name="from" type="text" value="" label="From" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	171 <param name="to" type="text" value="" label="To" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	172 </when>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	173 </conditional>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	174 </when>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	175 <when value="sequence">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	176 <conditional name="manipulation">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	177 <param name="manipulation_selector" type="select" label="Sequence Manipulation Type">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	178 <option value="rev_comp">Reverse Complement</option>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	179 <option value="rev_no_comp">Reverse, No Complement</option>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	180 <option value="no_rev_comp">Complement, No Reverse</option>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	181 <option value="trim">Trim</option>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	182 <option value="dna_to_rna">DNA to RNA</option>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	183 <option value="rna_to_dna">RNA to DNA</option>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	184 <option value="translate">String Translate</option>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	185 <option value="change_adapter">Change Adapter Base</option>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	186 </param>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	187 <when value="rev_comp" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	188 <when value="rev_no_comp" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	189 <when value="no_rev_comp" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	190 <when value="trim">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	191 <conditional name="offset_type">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	192 <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Use Absolute for fixed length reads (Illumina, SOLiD)<br>Use Percentage for variable length reads (Roche/454)">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	193 <option value="offsets_absolute" selected="true">Absolute Values</option>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	194 <option value="offsets_percent">Percentage of Read Length</option>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	195 </param>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	196 <when value="offsets_absolute">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	197 <param name="left_column_offset" type="integer" min="0" value="0" label="Offset from 5' end" help="Values start at 0, increasing from the left" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	198 <param name="right_column_offset" type="integer" value="0" label="Offset from 3' end" help="Values start at 0, increasing from the right; use a negative value to remove everything to the right of the absolute value of the position" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	199 </when>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	200 <when value="offsets_percent">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	201 <param name="left_column_offset" type="float" min="0" max="100" value="0" label="Offset from 5' end" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	202 <param name="right_column_offset" type="float" min="0" max="100" value="0" label="Offset from 3' end" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	203 </when>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	204 </conditional>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	205 <param name="keep_zero_length" type="boolean" truevalue="keep_zero_length" falsevalue="exclude_zero_length" checked="false" label="Keep reads with zero length" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	206 </when>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	207 <when value="dna_to_rna" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	208 <when value="rna_to_dna" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	209 <when value="translate">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	210 <param name="from" type="text" value="" label="From" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	211 <param name="to" type="text" value="" label="To" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	212 </when>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	213 <when value="change_adapter">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	214 <param name="new_adapter" type="text" value="G" label="New adapter" help="An empty string will remove the adapter base" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	215 </when>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	216 </conditional>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	217 </when>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	218 <when value="quality">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	219 <conditional name="manipulation">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	220 <param name="manipulation_selector" type="select" label="Quality Manipulation Type">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	221 <option value="translate">String Translate</option>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	222 <!-- <option value="modify_each_score">Apply Transformation to each Score</option> Not enabled yet-->
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	223 </param>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	224 <when value="translate">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	225 <param name="from" type="text" value="" label="From" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	226 <param name="to" type="text" value="" label="To" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	227 </when>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	228 <!-- <when value="modify_each_score">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	229 <param name="map_score" type="text" label="Modify Score by" value="$score + 1" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	230 </when> -->
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	231 </conditional>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	232 </when>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	233 <when value="miscellaneous">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	234 <conditional name="manipulation">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	235 <param name="manipulation_selector" type="select" label="Miscellaneous Manipulation Type">
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	236 <option value="remove">Remove Read</option>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	237 </param>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	238 <when value="remove" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	239 </conditional>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	240 </when>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	241 </conditional>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	242 </repeat>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	243 </inputs>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	244 <outputs>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	245 <data name="output_file" format_source="input_file" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	246 </outputs>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	247 <tests>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	248 <!-- match all and do nothing -->
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	249 <test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	250 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
7 3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	251 <repeat name="match_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	252 <conditional name="match_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	253 <param name="match_type_selector" value="identifier" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	254 <conditional name="match">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	255 <param name="match_selector" value="regex" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	256 <param name="match_by" value=".*" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	257 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	258 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	259 </repeat>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	260 <repeat name="manipulate_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	261 <conditional name="manipulation_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	262 <param name="manipulation_type_selector" value="identifier" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	263 <conditional name="manipulation">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	264 <param name="manipulation_selector" value="translate" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	265 <param name="from" value="" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	266 <param name="to" value="" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	267 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	268 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	269 </repeat>
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	270 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	271 </test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	272 <!-- match None and do nothing -->
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	273 <test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	274 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
7 3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	275 <repeat name="match_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	276 <conditional name="match_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	277 <param name="match_type_selector" value="identifier" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	278 <conditional name="match">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	279 <param name="match_selector" value="regex" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	280 <param name="match_by" value="STRINGDOESNOTEXIST" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	281 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	282 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	283 </repeat>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	284 <repeat name="manipulate_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	285 <conditional name="manipulation_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	286 <param name="manipulation_type_selector" value="identifier" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	287 <conditional name="manipulation">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	288 <param name="manipulation_selector" value="translate" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	289 <param name="from" value="" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	290 <param name="to" value="" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	291 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	292 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	293 </repeat>
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	294 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	295 </test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	296 <!-- match all and remove -->
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	297 <test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	298 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
7 3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	299 <repeat name="match_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	300 <conditional name="match_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	301 <param name="match_type_selector" value="identifier" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	302 <conditional name="match">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	303 <param name="match_selector" value="regex" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	304 <param name="match_by" value=".*" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	305 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	306 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	307 </repeat>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	308 <repeat name="manipulate_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	309 <conditional name="manipulation_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	310 <param name="manipulation_type_selector" value="miscellaneous" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	311 <conditional name="manipulation">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	312 <param name="manipulation_selector" value="remove" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	313 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	314 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	315 </repeat>
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	316 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	317 </test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	318 <!-- match None and remove -->
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	319 <test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	320 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
7 3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	321 <repeat name="match_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	322 <conditional name="match_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	323 <param name="match_type_selector" value="identifier" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	324 <conditional name="match">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	325 <param name="match_selector" value="regex" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	326 <param name="match_by" value="STRINGDOESNOTEXIST" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	327 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	328 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	329 </repeat>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	330 <repeat name="manipulate_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	331 <conditional name="manipulation_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	332 <param name="manipulation_type_selector" value="miscellaneous" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	333 <conditional name="manipulation">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	334 <param name="manipulation_selector" value="remove" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	335 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	336 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	337 </repeat>
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	338 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	339 </test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	340 <!-- match all and trim to 4 inner-most bases -->
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	341 <test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	342 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
7 3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	343 <repeat name="match_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	344 <conditional name="match_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	345 <param name="match_type_selector" value="identifier" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	346 <conditional name="match">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	347 <param name="match_selector" value="regex" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	348 <param name="match_by" value=".*" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	349 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	350 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	351 </repeat>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	352 <repeat name="manipulate_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	353 <conditional name="manipulation_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	354 <param name="manipulation_type_selector" value="sequence" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	355 <conditional name="manipulation">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	356 <param name="manipulation_selector" value="trim" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	357 <conditional name="offset_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	358 <param name="base_offset_type" value="offsets_absolute"/>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	359 <param name="left_column_offset" value="45"/>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	360 <param name="right_column_offset" value="45"/>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	361 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	362 <param name="keep_zero_length" value="true" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	363 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	364 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	365 </repeat>
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	366 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	367 </test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	368 <test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	369 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
7 3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	370 <repeat name="match_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	371 <conditional name="match_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	372 <param name="match_type_selector" value="identifier" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	373 <conditional name="match">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	374 <param name="match_selector" value="regex" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	375 <param name="match_by" value=".*" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	376 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	377 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	378 </repeat>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	379 <repeat name="manipulate_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	380 <conditional name="manipulation_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	381 <param name="manipulation_type_selector" value="sequence" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	382 <conditional name="manipulation">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	383 <param name="manipulation_selector" value="trim" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	384 <conditional name="offset_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	385 <param name="base_offset_type" value="offsets_percent"/>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	386 <param name="left_column_offset" value="47.87"/>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	387 <param name="right_column_offset" value="47.87"/>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	388 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	389 <param name="keep_zero_length" value="true" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	390 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	391 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	392 </repeat>
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	393 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	394 </test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	395 <!-- match all and rev comp -->
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	396 <test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	397 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
7 3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	398 <repeat name="match_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	399 <conditional name="match_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	400 <param name="match_type_selector" value="identifier" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	401 <conditional name="match">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	402 <param name="match_selector" value="regex" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	403 <param name="match_by" value=".*" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	404 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	405 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	406 </repeat>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	407 <repeat name="manipulate_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	408 <conditional name="manipulation_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	409 <param name="manipulation_type_selector" value="sequence" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	410 <conditional name="manipulation">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	411 <param name="manipulation_selector" value="rev_comp" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	412 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	413 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	414 </repeat>
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	415 <output name="output_file" file="sanger_full_range_rev_comp.fastqsanger" ftype="fastqsanger" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	416 </test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	417 <!-- match all and rev comp, with ambiguous DNA -->
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	418 <test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	419 <param name="input_file" value="misc_dna_original_sanger.fastqsanger" ftype="fastqsanger" />
7 3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	420 <repeat name="match_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	421 <conditional name="match_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	422 <param name="match_type_selector" value="identifier" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	423 <conditional name="match">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	424 <param name="match_selector" value="regex" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	425 <param name="match_by" value=".*" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	426 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	427 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	428 </repeat>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	429 <repeat name="manipulate_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	430 <conditional name="manipulation_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	431 <param name="manipulation_type_selector" value="sequence" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	432 <conditional name="manipulation">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	433 <param name="manipulation_selector" value="rev_comp" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	434 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	435 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	436 </repeat>
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	437 <output name="output_file" file="misc_dna_as_sanger_rev_comp_1.fastqsanger" ftype="fastqsanger" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	438 </test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	439 <!-- match all and rev comp, with ambiguous RNA -->
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	440 <test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	441 <param name="input_file" value="misc_rna_original_sanger.fastqsanger" ftype="fastqsanger" />
7 3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	442 <repeat name="match_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	443 <conditional name="match_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	444 <param name="match_type_selector" value="identifier" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	445 <conditional name="match">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	446 <param name="match_selector" value="regex" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	447 <param name="match_by" value=".*" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	448 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	449 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	450 </repeat>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	451 <repeat name="manipulate_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	452 <conditional name="manipulation_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	453 <param name="manipulation_type_selector" value="sequence" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	454 <conditional name="manipulation">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	455 <param name="manipulation_selector" value="rev_comp" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	456 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	457 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	458 </repeat>
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	459 <output name="output_file" file="misc_rna_as_sanger_rev_comp_1.fastqsanger" ftype="fastqsanger" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	460 </test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	461 <!-- match first seq and rev comp -->
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	462 <test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	463 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
7 3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	464 <repeat name="match_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	465 <conditional name="match_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	466 <param name="match_type_selector" value="identifier" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	467 <conditional name="match">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	468 <param name="match_selector" value="regex" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	469 <param name="match_by" value="FAKE0001" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	470 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	471 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	472 </repeat>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	473 <repeat name="manipulate_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	474 <conditional name="manipulation_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	475 <param name="manipulation_type_selector" value="sequence" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	476 <conditional name="manipulation">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	477 <param name="manipulation_selector" value="rev_comp" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	478 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	479 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	480 </repeat>
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	481 <output name="output_file" file="sanger_full_range_rev_comp_1_seq.fastqsanger" ftype="fastqsanger" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	482 </test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	483 <!-- match first seq and rev comp: i.e. undo above -->
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	484 <test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	485 <param name="input_file" value="sanger_full_range_rev_comp_1_seq.fastqsanger" ftype="fastqsanger" />
7 3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	486 <repeat name="match_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	487 <conditional name="match_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	488 <param name="match_type_selector" value="identifier" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	489 <conditional name="match">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	490 <param name="match_selector" value="regex" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	491 <param name="match_by" value="FAKE0001" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	492 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	493 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	494 </repeat>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	495 <repeat name="manipulate_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	496 <conditional name="manipulation_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	497 <param name="manipulation_type_selector" value="sequence" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	498 <conditional name="manipulation">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	499 <param name="manipulation_selector" value="rev_comp" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	500 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	501 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	502 </repeat>
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	503 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	504 </test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	505 <!-- match all and DNA to RNA -->
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	506 <test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	507 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
7 3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	508 <repeat name="match_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	509 <conditional name="match_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	510 <param name="match_type_selector" value="identifier" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	511 <conditional name="match">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	512 <param name="match_selector" value="regex" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	513 <param name="match_by" value=".*" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	514 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	515 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	516 </repeat>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	517 <repeat name="manipulate_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	518 <conditional name="manipulation_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	519 <param name="manipulation_type_selector" value="sequence" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	520 <conditional name="manipulation">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	521 <param name="manipulation_selector" value="dna_to_rna" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	522 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	523 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	524 </repeat>
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	525 <output name="output_file" file="sanger_full_range_as_rna.fastqsanger" ftype="fastqsanger" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	526 </test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	527 <!-- match all and RNA to DNA-->
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	528 <test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	529 <param name="input_file" value="sanger_full_range_as_rna.fastqsanger" ftype="fastqsanger" />
7 3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	530 <repeat name="match_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	531 <conditional name="match_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	532 <param name="match_type_selector" value="identifier" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	533 <conditional name="match">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	534 <param name="match_selector" value="regex" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	535 <param name="match_by" value=".*" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	536 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	537 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	538 </repeat>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	539 <repeat name="manipulate_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	540 <conditional name="manipulation_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	541 <param name="manipulation_type_selector" value="sequence" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	542 <conditional name="manipulation">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	543 <param name="manipulation_selector" value="rna_to_dna" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	544 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	545 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	546 </repeat>
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	547 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	548 </test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	549 <!-- match all and RNA to DNA (gz compressed) -->
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	550 <test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	551 <param name="input_file" value="sanger_full_range_as_rna.fastqsanger.gz" ftype="fastqsanger.gz" />
7 3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	552 <repeat name="match_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	553 <conditional name="match_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	554 <param name="match_type_selector" value="identifier" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	555 <conditional name="match">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	556 <param name="match_selector" value="regex" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	557 <param name="match_by" value=".*" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	558 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	559 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	560 </repeat>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	561 <repeat name="manipulate_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	562 <conditional name="manipulation_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	563 <param name="manipulation_type_selector" value="sequence" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	564 <conditional name="manipulation">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	565 <param name="manipulation_selector" value="rna_to_dna" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	566 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	567 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	568 </repeat>
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	569 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	570 </test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	571 <!-- match all and RNA to DNA (bz2 compressed) -->
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	572 <test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	573 <param name="input_file" value="sanger_full_range_as_rna.fastqsanger.bz2" ftype="fastqsanger.bz2" />
7 3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	574 <repeat name="match_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	575 <conditional name="match_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	576 <param name="match_type_selector" value="identifier" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	577 <conditional name="match">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	578 <param name="match_selector" value="regex" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	579 <param name="match_by" value=".*" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	580 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	581 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	582 </repeat>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	583 <repeat name="manipulate_blocks">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	584 <conditional name="manipulation_type">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	585 <param name="manipulation_type_selector" value="sequence" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	586 <conditional name="manipulation">
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	587 <param name="manipulation_selector" value="rna_to_dna" />
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	588 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	589 </conditional>
3b9ecb0920bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	590 </repeat>
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	591 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	592 </test>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	593 </tests>
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	594 <help><![CDATA[
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	595 This tool allows you to build complex manipulations to be applied to each matching read in a FASTQ file. A read must match all matching directives in order for it to be manipulated; if a read does not match, it is output in a non-modified manner. All reads matching will have each of the specified manipulations performed upon them, in the order specified.
de14b969d713 Imported from capsule None devteam parents: diff changeset	596
de14b969d713 Imported from capsule None devteam parents: diff changeset	597 Regular Expression Matches are made using re.search, see http://docs.python.org/library/re.html for more information.
de14b969d713 Imported from capsule None devteam parents: diff changeset	598 All matching is performed on a single line string, regardless if e.g. the sequence or quality score spans multiple lines in the original file.
de14b969d713 Imported from capsule None devteam parents: diff changeset	599
de14b969d713 Imported from capsule None devteam parents: diff changeset	600 String translations are performed using string.translate, see http://docs.python.org/library/string.html#string.translate and http://docs.python.org/library/string.html#string.maketrans for more information.
de14b969d713 Imported from capsule None devteam parents: diff changeset	601
de14b969d713 Imported from capsule None devteam parents: diff changeset	602 .. class:: warningmark
de14b969d713 Imported from capsule None devteam parents: diff changeset	603
de14b969d713 Imported from capsule None devteam parents: diff changeset	604 Only color space reads can have adapter bases substituted.
de14b969d713 Imported from capsule None devteam parents: diff changeset	605
de14b969d713 Imported from capsule None devteam parents: diff changeset	606 -----
de14b969d713 Imported from capsule None devteam parents: diff changeset	607
de14b969d713 Imported from capsule None devteam parents: diff changeset	608 Example
de14b969d713 Imported from capsule None devteam parents: diff changeset	609
de14b969d713 Imported from capsule None devteam parents: diff changeset	610 Suppose you have a color space sanger formatted sequence (fastqcssanger) and you want to double-encode the color space into psuedo-nucleotide space (this is different from converting) to allow these reads to be used in tools which do not natively support it (using specially designed indexes). This tool can handle this manipulation, however, this is generally not recommended as results tend to be poorer than those produced from tools which are specially designed to handle color space data.
de14b969d713 Imported from capsule None devteam parents: diff changeset	611
de14b969d713 Imported from capsule None devteam parents: diff changeset	612 Steps:
de14b969d713 Imported from capsule None devteam parents: diff changeset	613
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	614 1. Click Add new Match Reads and leave the matching options set to the default (Matching by sequence name/identifier using the regular expression "\*."; thereby matching all reads).
7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	615 2. Click Add new Manipulate Reads, change Manipulate Reads on to "Sequence Content", set Sequence Manipulation Type to "Change Adapter Base" and set New Adapter to "" (an empty text field).
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	616 3. Click Add new Manipulate Reads, change Manipulate Reads on to "Sequence Content", set Sequence Manipulation Type to "String Translate" and set From to "0123." and To to "ACGTN".
de14b969d713 Imported from capsule None devteam parents: diff changeset	617 4. Click Execute. The new history item will contained double-encoded psuedo-nucleotide space reads.
3 7ea141c4c834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 2 diff changeset	618 ]]></help>
1 b50aeae8bcaa planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	619 <citations>
b50aeae8bcaa planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	620 <citation type="doi">10.1093/bioinformatics/btq281</citation>
b50aeae8bcaa planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 0 diff changeset	621 </citations>
0 de14b969d713 Imported from capsule None devteam parents: diff changeset	622 </tool>

Mercurial > repos > devteam > fastq_manipulation

annotate fastq_manipulation.xml @ 7:3b9ecb0920bf draft default tip