annotate fastq_manipulation.xml @ 2:4ac14b275aca draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
author devteam
date Sat, 30 Sep 2017 14:58:21 -0400
parents bb07615a5b6a
children 7861f3b10c68
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
1 <tool id="fastq_manipulation" name="Manipulate FASTQ" version="1.1.1">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
2 <options sanitize="false" /> <!-- This tool uses a file to rely all parameter information (actually a dynamically generated python module), we can safely not sanitize any parameters -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
3 <description>reads on various attributes</description>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
4 <requirements>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
5 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
6 </requirements>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
7 <command><![CDATA[
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
8 gx-fastq-manipulation '$input_file' '$fastq_manipulation_file' '$output_file' '$output_file.files_path' '${input_file.extension[len('fastq'):]}'
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
9 ]]></command>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
10 <configfiles>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
11 <configfile name="fastq_manipulation_file"><![CDATA[##create an importable module
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
12 #import binascii
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
13 import binascii
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
14 import re
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
15 import six
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
16
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
17 if six.PY2:
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
18 from string import maketrans
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
19 else:
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
20 maketrans = str.maketrans
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
21
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
22
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
23 ##does read match
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
24 def match_read(fastq_read):
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
25 #for $match_block in $match_blocks:
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
26 #if $match_block['match_type']['match_type_selector'] == 'identifier':
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
27 search_target = fastq_read.identifier[1:] ##don't include @
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
28 #elif $match_block['match_type']['match_type_selector'] == 'sequence':
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
29 search_target = fastq_read.sequence
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
30 #elif $match_block['match_type']['match_type_selector'] == 'quality':
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
31 search_target = fastq_read.quality
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
32 #else:
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
33 #continue
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
34 #end if
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
35 if not re.search(binascii.unhexlify("${ binascii.hexlify(str(match_block['match_type']['match']['match_by'])) }").decode(), search_target):
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
36 return False
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
37 #end for
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
38 return True
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
39
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
40
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
41 ##modify matched reads
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
42 def manipulate_read(fastq_read):
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
43 new_read = fastq_read.clone()
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
44 #for $manipulate_block in $manipulate_blocks:
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
45 #if $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'identifier':
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
46 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'translate':
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
47 new_read.identifier = "@%s" % new_read.identifier[1:].translate(maketrans(binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from'])) }").decode(), binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to'])) }").decode()))
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
48 #end if
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
49 #elif $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'sequence':
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
50 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'translate':
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
51 new_read.sequence = new_read.sequence.translate(maketrans(binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from'])) }").decode(), binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to'])) }").decode()))
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
52 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'rev_comp':
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
53 new_read = new_read.reverse_complement()
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
54 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'rev_no_comp':
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
55 new_read = new_read.reverse()
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
56 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'no_rev_comp':
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
57 new_read = new_read.complement()
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
58 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'trim':
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
59 #if $manipulate_block['manipulation_type']['manipulation']['offset_type']['base_offset_type'] == 'offsets_percent':
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
60 left_column_offset = int(round(float(${ manipulate_block['manipulation_type']['manipulation']['offset_type']['left_column_offset'] }) / 100.0 * float(len(new_read))))
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
61 right_column_offset = int(round(float(${ manipulate_block['manipulation_type']['manipulation']['offset_type']['right_column_offset'] }) / 100.0 * float(len(new_read))))
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
62 #else
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
63 left_column_offset = ${ manipulate_block['manipulation_type']['manipulation']['offset_type']['left_column_offset'] }
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
64 right_column_offset = ${ manipulate_block['manipulation_type']['manipulation']['offset_type']['right_column_offset'] }
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
65 #end if
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
66 if right_column_offset != 0:
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
67 right_column_offset = -right_column_offset
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
68 else:
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
69 right_column_offset = None
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
70 new_read = new_read.slice(left_column_offset, right_column_offset)
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
71 if not (${str(manipulate_block['manipulation_type']['manipulation']['keep_zero_length']) == 'keep_zero_length'} or len(new_read)):
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
72 return None
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
73 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'dna_to_rna':
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
74 new_read = new_read.sequence_as_DNA()
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
75 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'rna_to_dna':
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
76 new_read = new_read.sequence_as_RNA()
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
77 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'change_adapter':
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
78 if new_read.sequence_space == 'color':
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
79 new_read = new_read.change_adapter(binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['new_adapter'])) }").decode())
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
80 #end if
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
81 #elif $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'quality':
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
82 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'translate':
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
83 new_read.quality = new_read.quality.translate(maketrans(binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from'])) }").decode(), binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to'])) }").decode()))
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
84 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'map_score':
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
85 def score_method(score):
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
86 raise Exception("Unimplemented") ##This option is not yet available, need to abstract out e.g. column adding tool action: preventing users from using 'harmful' actions
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
87 new_read.quality_map(score_method)
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
88 #end if
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
89 #elif $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'miscellaneous':
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
90 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'remove':
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
91 return None
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
92 #end if
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
93 #else:
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
94 #continue
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
95 #end if
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
96 #end for
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
97 if new_read.description != "+":
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
98 new_read.description = "+%s" % new_read.identifier[1:] ##ensure description is still valid
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
99 return new_read
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
100
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
101
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
102 def match_and_manipulate_read(fastq_read):
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
103 new_read = fastq_read
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
104 if match_read(fastq_read):
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
105 new_read = manipulate_read(fastq_read)
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
106 return new_read
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
107 ]]></configfile>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
108 </configfiles>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
109 <inputs>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
110 <!-- This tool is purposely over-engineered (e.g. Single option conditionals) to allow easy enhancement with workflow/rerun compatibility -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
111 <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ File" help="Requires groomed data: if your data does not appear here try using the FASTQ groomer"/>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
112 <!-- Match Reads -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
113 <repeat name="match_blocks" title="Match Reads">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
114 <conditional name="match_type">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
115 <param name="match_type_selector" type="select" label="Match Reads by">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
116 <option value="identifier">Name/Identifier</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
117 <option value="sequence">Sequence Content</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
118 <option value="quality">Quality Score Content</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
119 </param>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
120 <when value="identifier">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
121 <conditional name="match">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
122 <param name="match_selector" type="select" label="Identifier Match Type">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
123 <option value="regex">Regular Expression</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
124 </param>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
125 <when value="regex">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
126 <param name="match_by" type="text" value=".*" label="Match by" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
127 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
128 </conditional>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
129 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
130 <when value="sequence">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
131 <conditional name="match">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
132 <param name="match_selector" type="select" label="Sequence Match Type">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
133 <option value="regex">Regular Expression</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
134 </param>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
135 <when value="regex">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
136 <param name="match_by" type="text" value=".*" label="Match by" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
137 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
138 </conditional>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
139 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
140 <when value="quality">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
141 <conditional name="match">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
142 <param name="match_selector" type="select" label="Quality Match Type">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
143 <option value="regex">Regular Expression</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
144 </param>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
145 <when value="regex">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
146 <param name="match_by" type="text" value=".*" label="Match by" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
147 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
148 </conditional>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
149 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
150 </conditional>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
151 </repeat>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
152 <!-- Manipulate Matched Reads -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
153 <repeat name="manipulate_blocks" title="Manipulate Reads">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
154 <conditional name="manipulation_type">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
155 <param name="manipulation_type_selector" type="select" label="Manipulate Reads on">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
156 <option value="identifier">Name/Identifier</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
157 <option value="sequence">Sequence Content</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
158 <option value="quality">Quality Score Content</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
159 <option value="miscellaneous">Miscellaneous Actions</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
160 </param>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
161 <when value="identifier">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
162 <conditional name="manipulation">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
163 <param name="manipulation_selector" type="select" label="Identifier Manipulation Type">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
164 <option value="translate">String Translate</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
165 </param>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
166 <when value="translate">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
167 <param name="from" type="text" value="" label="From" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
168 <param name="to" type="text" value="" label="To" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
169 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
170 </conditional>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
171 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
172 <when value="sequence">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
173 <conditional name="manipulation">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
174 <param name="manipulation_selector" type="select" label="Sequence Manipulation Type">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
175 <option value="rev_comp">Reverse Complement</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
176 <option value="rev_no_comp">Reverse, No Complement</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
177 <option value="no_rev_comp">Complement, No Reverse</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
178 <option value="trim">Trim</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
179 <option value="dna_to_rna">DNA to RNA</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
180 <option value="rna_to_dna">RNA to DNA</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
181 <option value="translate">String Translate</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
182 <option value="change_adapter">Change Adapter Base</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
183 </param>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
184 <when value="rev_comp" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
185 <when value="rev_no_comp" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
186 <when value="no_rev_comp" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
187 <when value="trim">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
188 <conditional name="offset_type">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
189 <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Use Absolute for fixed length reads (Illumina, SOLiD)&lt;br&gt;Use Percentage for variable length reads (Roche/454)">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
190 <option value="offsets_absolute" selected="true">Absolute Values</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
191 <option value="offsets_percent">Percentage of Read Length</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
192 </param>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
193 <when value="offsets_absolute">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
194 <param name="left_column_offset" type="integer" min="0" value="0" label="Offset from 5' end" help="Values start at 0, increasing from the left" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
195 <param name="right_column_offset" type="integer" value="0" label="Offset from 3' end" help="Values start at 0, increasing from the right; use a negative value to remove everything to the right of the absolute value of the position" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
196 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
197 <when value="offsets_percent">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
198 <param name="left_column_offset" type="float" min="0" max="100" value="0" label="Offset from 5' end" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
199 <param name="right_column_offset" type="float" min="0" max="100" value="0" label="Offset from 3' end" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
200 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
201 </conditional>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
202 <param name="keep_zero_length" type="boolean" truevalue="keep_zero_length" falsevalue="exclude_zero_length" checked="false" label="Keep reads with zero length" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
203 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
204 <when value="dna_to_rna" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
205 <when value="rna_to_dna" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
206 <when value="translate">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
207 <param name="from" type="text" value="" label="From" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
208 <param name="to" type="text" value="" label="To" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
209 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
210 <when value="change_adapter">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
211 <param name="new_adapter" type="text" value="G" label="New adapter" help="An empty string will remove the adapter base" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
212 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
213 </conditional>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
214 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
215 <when value="quality">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
216 <conditional name="manipulation">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
217 <param name="manipulation_selector" type="select" label="Quality Manipulation Type">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
218 <option value="translate">String Translate</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
219 <!-- <option value="modify_each_score">Apply Transformation to each Score</option> Not enabled yet-->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
220 </param>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
221 <when value="translate">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
222 <param name="from" type="text" value="" label="From" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
223 <param name="to" type="text" value="" label="To" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
224 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
225 <!-- <when value="modify_each_score">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
226 <param name="map_score" type="text" label="Modify Score by" value="$score + 1" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
227 </when> -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
228 </conditional>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
229 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
230 <when value="miscellaneous">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
231 <conditional name="manipulation">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
232 <param name="manipulation_selector" type="select" label="Miscellaneous Manipulation Type">
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
233 <option value="remove">Remove Read</option>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
234 </param>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
235 <when value="remove" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
236 </conditional>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
237 </when>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
238 </conditional>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
239 </repeat>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
240 </inputs>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
241 <outputs>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
242 <data name="output_file" format_source="input_file" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
243 </outputs>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
244 <tests>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
245 <!-- match all and do nothing -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
246 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
247 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
248 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
249 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
250 <param name="match_by" value=".*" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
251 <param name="manipulation_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
252 <param name="manipulation_selector" value="translate" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
253 <param name="from" value="" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
254 <param name="to" value="" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
255 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
256 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
257 <!-- match None and do nothing -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
258 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
259 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
260 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
261 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
262 <param name="match_by" value="STRINGDOESNOTEXIST" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
263 <param name="manipulation_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
264 <param name="manipulation_selector" value="translate" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
265 <param name="from" value="" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
266 <param name="to" value="" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
267 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
268 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
269 <!-- match all and remove -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
270 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
271 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
272 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
273 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
274 <param name="match_by" value=".*" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
275 <param name="manipulation_type_selector" value="miscellaneous" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
276 <param name="manipulation_selector" value="remove" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
277 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
278 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
279 <!-- match None and remove -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
280 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
281 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
282 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
283 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
284 <param name="match_by" value="STRINGDOESNOTEXIST" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
285 <param name="manipulation_type_selector" value="miscellaneous" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
286 <param name="manipulation_selector" value="remove" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
287 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
288 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
289 <!-- match all and trim to 4 inner-most bases -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
290 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
291 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
292 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
293 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
294 <param name="match_by" value=".*" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
295 <param name="manipulation_type_selector" value="sequence" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
296 <param name="manipulation_selector" value="trim" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
297 <param name="base_offset_type" value="offsets_absolute"/>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
298 <param name="left_column_offset" value="45"/>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
299 <param name="right_column_offset" value="45"/>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
300 <param name="keep_zero_length" value="true" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
301 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
302 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
303 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
304 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
305 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
306 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
307 <param name="match_by" value=".*" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
308 <param name="manipulation_type_selector" value="sequence" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
309 <param name="manipulation_selector" value="trim" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
310 <param name="base_offset_type" value="offsets_percent"/>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
311 <param name="left_column_offset" value="47.87"/>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
312 <param name="right_column_offset" value="47.87"/>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
313 <param name="keep_zero_length" value="true" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
314 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
315 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
316 <!-- match all and rev comp -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
317 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
318 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
319 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
320 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
321 <param name="match_by" value=".*" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
322 <param name="manipulation_type_selector" value="sequence" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
323 <param name="manipulation_selector" value="rev_comp" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
324 <output name="output_file" file="sanger_full_range_rev_comp.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
325 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
326 <!-- match all and rev comp, with ambiguous DNA -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
327 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
328 <param name="input_file" value="misc_dna_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
329 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
330 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
331 <param name="match_by" value=".*" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
332 <param name="manipulation_type_selector" value="sequence" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
333 <param name="manipulation_selector" value="rev_comp" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
334 <output name="output_file" file="misc_dna_as_sanger_rev_comp_1.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
335 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
336 <!-- match all and rev comp, with ambiguous RNA -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
337 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
338 <param name="input_file" value="misc_rna_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
339 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
340 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
341 <param name="match_by" value=".*" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
342 <param name="manipulation_type_selector" value="sequence" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
343 <param name="manipulation_selector" value="rev_comp" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
344 <output name="output_file" file="misc_rna_as_sanger_rev_comp_1.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
345 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
346 <!-- match first seq and rev comp -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
347 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
348 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
349 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
350 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
351 <param name="match_by" value="FAKE0001" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
352 <param name="manipulation_type_selector" value="sequence" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
353 <param name="manipulation_selector" value="rev_comp" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
354 <output name="output_file" file="sanger_full_range_rev_comp_1_seq.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
355 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
356 <!-- match first seq and rev comp: i.e. undo above -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
357 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
358 <param name="input_file" value="sanger_full_range_rev_comp_1_seq.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
359 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
360 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
361 <param name="match_by" value="FAKE0001" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
362 <param name="manipulation_type_selector" value="sequence" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
363 <param name="manipulation_selector" value="rev_comp" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
364 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
365 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
366 <!-- match all and DNA to RNA -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
367 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
368 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
369 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
370 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
371 <param name="match_by" value=".*" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
372 <param name="manipulation_type_selector" value="sequence" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
373 <param name="manipulation_selector" value="dna_to_rna" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
374 <output name="output_file" file="sanger_full_range_as_rna.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
375 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
376 <!-- match all and RNA to DNA-->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
377 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
378 <param name="input_file" value="sanger_full_range_as_rna.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
379 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
380 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
381 <param name="match_by" value=".*" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
382 <param name="manipulation_type_selector" value="sequence" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
383 <param name="manipulation_selector" value="rna_to_dna" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
384 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
385 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
386 <!-- match all and RNA to DNA (gz compressed) -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
387 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
388 <param name="input_file" value="sanger_full_range_as_rna.fastqsanger.gz" ftype="fastqsanger.gz" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
389 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
390 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
391 <param name="match_by" value=".*" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
392 <param name="manipulation_type_selector" value="sequence" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
393 <param name="manipulation_selector" value="rna_to_dna" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
394 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
395 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
396 <!-- match all and RNA to DNA (bz2 compressed) -->
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
397 <test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
398 <param name="input_file" value="sanger_full_range_as_rna.fastqsanger.bz2" ftype="fastqsanger.bz2" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
399 <param name="match_type_selector" value="identifier" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
400 <param name="match_selector" value="regex" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
401 <param name="match_by" value=".*" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
402 <param name="manipulation_type_selector" value="sequence" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
403 <param name="manipulation_selector" value="rna_to_dna" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
404 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
405 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
406 </tests>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
407 <help><![CDATA[
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
408 This tool allows you to build complex manipulations to be applied to each matching read in a FASTQ file. A read must match all matching directives in order for it to be manipulated; if a read does not match, it is output in a non-modified manner. All reads matching will have each of the specified manipulations performed upon them, in the order specified.
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
409
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
410 Regular Expression Matches are made using re.search, see http://docs.python.org/library/re.html for more information.
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
411 All matching is performed on a single line string, regardless if e.g. the sequence or quality score spans multiple lines in the original file.
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
412
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
413 String translations are performed using string.translate, see http://docs.python.org/library/string.html#string.translate and http://docs.python.org/library/string.html#string.maketrans for more information.
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
414
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
415 .. class:: warningmark
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
416
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
417 Only color space reads can have adapter bases substituted.
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
418
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
419 -----
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
420
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
421 **Example**
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
422
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
423 Suppose you have a color space sanger formatted sequence (fastqcssanger) and you want to double-encode the color space into psuedo-nucleotide space (this is different from converting) to allow these reads to be used in tools which do not natively support it (using specially designed indexes). This tool can handle this manipulation, however, this is generally not recommended as results tend to be poorer than those produced from tools which are specially designed to handle color space data.
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
424
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
425 Steps:
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
426
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
427 1. Click **Add new Match Reads** and leave the matching options set to the default (Matching by sequence name/identifier using the regular expression "\*."; thereby matching all reads).
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
428 2. Click **Add new Manipulate Reads**, change **Manipulate Reads on** to "Sequence Content", set **Sequence Manipulation Type** to "Change Adapter Base" and set **New Adapter** to "" (an empty text field).
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
429 3. Click **Add new Manipulate Reads**, change **Manipulate Reads on** to "Sequence Content", set **Sequence Manipulation Type** to "String Translate" and set **From** to "0123." and **To** to "ACGTN".
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
430 4. Click Execute. The new history item will contained double-encoded psuedo-nucleotide space reads.
2
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
431 ]]></help>
1
bb07615a5b6a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
432 <citations>
bb07615a5b6a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
433 <citation type="doi">10.1093/bioinformatics/btq281</citation>
bb07615a5b6a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
434 </citations>
0
5d1e9e13e8db Imported from capsule None
devteam
parents:
diff changeset
435 </tool>