annotate fastq_manipulation.xml @ 4:5b87038565bb draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
author iuc
date Wed, 19 Feb 2020 12:31:39 -0500
parents 7861f3b10c68
children e30352e889fe
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rev   line source
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5b87038565bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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1 <tool id="fastq_manipulation" name="Manipulate FASTQ" version="@TOOL_VERSION@">
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2 <options sanitize="false" />
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3 <!-- This tool uses a file to rely all parameter information (actually a dynamically generated python module), we can safely not sanitize any parameters -->
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4 <description>reads on various attributes</description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <edam_topics>
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10 <edam_topic>topic_0622</edam_topic>
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11 </edam_topics>
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12 <edam_operations>
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13 <edam_operation>operation_0233</edam_operation>
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14 </edam_operations>
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15 <command><![CDATA[
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16 gx-fastq-manipulation '$input_file' '$fastq_manipulation_file' '$output_file' '$output_file.files_path' '${input_file.extension[len('fastq'):]}'
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17 ]]></command>
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18 <configfiles>
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19 <configfile name="fastq_manipulation_file"><![CDATA[##create an importable module
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20 #import binascii
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21 import binascii
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22 import re
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23 import six
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24
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25 if six.PY2:
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26 from string import maketrans
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27 else:
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28 maketrans = str.maketrans
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29
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30
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31 ##does read match
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32 def match_read(fastq_read):
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33 #for $match_block in $match_blocks:
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34 #if $match_block['match_type']['match_type_selector'] == 'identifier':
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35 search_target = fastq_read.identifier[1:] ##don't include @
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36 #elif $match_block['match_type']['match_type_selector'] == 'sequence':
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37 search_target = fastq_read.sequence
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38 #elif $match_block['match_type']['match_type_selector'] == 'quality':
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39 search_target = fastq_read.quality
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40 #else:
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41 #continue
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42 #end if
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43 if not re.search(binascii.unhexlify(${ binascii.hexlify(str(match_block['match_type']['match']['match_by']).encode()) }).decode(), search_target):
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44 return False
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45 #end for
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46 return True
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47
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48
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49 ##modify matched reads
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50 def manipulate_read(fastq_read):
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51 new_read = fastq_read.clone()
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52 #for $manipulate_block in $manipulate_blocks:
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53 #if $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'identifier':
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54 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'translate':
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55 new_read.identifier = "@%s" % new_read.identifier[1:].translate(maketrans(binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from']).encode()) }).decode(), binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to']).encode()) }).decode()))
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56 #end if
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57 #elif $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'sequence':
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58 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'translate':
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59 new_read.sequence = new_read.sequence.translate(maketrans(binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from']).encode()) }).decode(), binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to']).encode()) }).decode()))
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60 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'rev_comp':
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61 new_read = new_read.reverse_complement()
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62 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'rev_no_comp':
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63 new_read = new_read.reverse()
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64 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'no_rev_comp':
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65 new_read = new_read.complement()
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66 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'trim':
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67 #if $manipulate_block['manipulation_type']['manipulation']['offset_type']['base_offset_type'] == 'offsets_percent':
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68 left_column_offset = int(round(float(${ manipulate_block['manipulation_type']['manipulation']['offset_type']['left_column_offset'] }) / 100.0 * float(len(new_read))))
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69 right_column_offset = int(round(float(${ manipulate_block['manipulation_type']['manipulation']['offset_type']['right_column_offset'] }) / 100.0 * float(len(new_read))))
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70 #else
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71 left_column_offset = ${ manipulate_block['manipulation_type']['manipulation']['offset_type']['left_column_offset'] }
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72 right_column_offset = ${ manipulate_block['manipulation_type']['manipulation']['offset_type']['right_column_offset'] }
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73 #end if
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74 if right_column_offset != 0:
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75 right_column_offset = -right_column_offset
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76 else:
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77 right_column_offset = None
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78 new_read = new_read.slice(left_column_offset, right_column_offset)
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79 if not (${str(manipulate_block['manipulation_type']['manipulation']['keep_zero_length']) == 'keep_zero_length'} or len(new_read)):
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80 return None
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81 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'dna_to_rna':
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82 new_read = new_read.sequence_as_DNA()
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83 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'rna_to_dna':
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84 new_read = new_read.sequence_as_RNA()
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85 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'change_adapter':
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86 if new_read.sequence_space == 'color':
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87 new_read = new_read.change_adapter(binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['new_adapter']).encode()) }).decode())
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88 #end if
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89 #elif $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'quality':
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90 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'translate':
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91 new_read.quality = new_read.quality.translate(maketrans(binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from'])).encode() }).decode(), binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to']).encode()) }).decode()))
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92 #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'map_score':
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93 def score_method(score):
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94 raise Exception("Unimplemented") ##This option is not yet available, need to abstract out e.g. column adding tool action: preventing users from using 'harmful' actions
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95 new_read.quality_map(score_method)
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96 #end if
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97 #elif $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'miscellaneous':
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98 #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'remove':
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99 return None
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100 #end if
5d1e9e13e8db Imported from capsule None
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101 #else:
2
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102 #continue
0
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103 #end if
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104 #end for
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105 if new_read.description != "+":
2
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106 new_read.description = "+%s" % new_read.identifier[1:] ##ensure description is still valid
0
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107 return new_read
2
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108
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109
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110 def match_and_manipulate_read(fastq_read):
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111 new_read = fastq_read
2
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112 if match_read(fastq_read):
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113 new_read = manipulate_read(fastq_read)
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114 return new_read
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115 ]]></configfile>
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116 </configfiles>
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117 <inputs>
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118 <!-- This tool is purposely over-engineered (e.g. Single option conditionals) to allow easy enhancement with workflow/rerun compatibility -->
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119 <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ File" help="Requires groomed data: if your data does not appear here try using the FASTQ groomer"/>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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120 <!-- Match Reads -->
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121 <repeat name="match_blocks" title="Match Reads">
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122 <conditional name="match_type">
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123 <param name="match_type_selector" type="select" label="Match Reads by">
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124 <option value="identifier">Name/Identifier</option>
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125 <option value="sequence">Sequence Content</option>
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126 <option value="quality">Quality Score Content</option>
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127 </param>
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128 <when value="identifier">
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129 <conditional name="match">
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130 <param name="match_selector" type="select" label="Identifier Match Type">
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131 <option value="regex">Regular Expression</option>
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132 </param>
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133 <when value="regex">
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134 <param name="match_by" type="text" value=".*" label="Match by" />
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135 </when>
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136 </conditional>
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137 </when>
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138 <when value="sequence">
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139 <conditional name="match">
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140 <param name="match_selector" type="select" label="Sequence Match Type">
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141 <option value="regex">Regular Expression</option>
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142 </param>
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143 <when value="regex">
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144 <param name="match_by" type="text" value=".*" label="Match by" />
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145 </when>
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146 </conditional>
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147 </when>
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148 <when value="quality">
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149 <conditional name="match">
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150 <param name="match_selector" type="select" label="Quality Match Type">
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151 <option value="regex">Regular Expression</option>
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152 </param>
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153 <when value="regex">
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154 <param name="match_by" type="text" value=".*" label="Match by" />
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155 </when>
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156 </conditional>
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157 </when>
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158 </conditional>
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159 </repeat>
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160 <!-- Manipulate Matched Reads -->
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161 <repeat name="manipulate_blocks" title="Manipulate Reads">
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162 <conditional name="manipulation_type">
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163 <param name="manipulation_type_selector" type="select" label="Manipulate Reads on">
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164 <option value="identifier">Name/Identifier</option>
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165 <option value="sequence">Sequence Content</option>
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166 <option value="quality">Quality Score Content</option>
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167 <option value="miscellaneous">Miscellaneous Actions</option>
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168 </param>
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169 <when value="identifier">
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170 <conditional name="manipulation">
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171 <param name="manipulation_selector" type="select" label="Identifier Manipulation Type">
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172 <option value="translate">String Translate</option>
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173 </param>
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174 <when value="translate">
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175 <param name="from" type="text" value="" label="From" />
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176 <param name="to" type="text" value="" label="To" />
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177 </when>
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178 </conditional>
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179 </when>
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180 <when value="sequence">
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181 <conditional name="manipulation">
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182 <param name="manipulation_selector" type="select" label="Sequence Manipulation Type">
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183 <option value="rev_comp">Reverse Complement</option>
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184 <option value="rev_no_comp">Reverse, No Complement</option>
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185 <option value="no_rev_comp">Complement, No Reverse</option>
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186 <option value="trim">Trim</option>
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187 <option value="dna_to_rna">DNA to RNA</option>
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188 <option value="rna_to_dna">RNA to DNA</option>
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189 <option value="translate">String Translate</option>
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190 <option value="change_adapter">Change Adapter Base</option>
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191 </param>
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192 <when value="rev_comp" />
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193 <when value="rev_no_comp" />
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194 <when value="no_rev_comp" />
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195 <when value="trim">
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196 <conditional name="offset_type">
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197 <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)">
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198 <option value="offsets_absolute" selected="true">Absolute Values</option>
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199 <option value="offsets_percent">Percentage of Read Length</option>
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200 </param>
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201 <when value="offsets_absolute">
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202 <param name="left_column_offset" type="integer" min="0" value="0" label="Offset from 5' end" help="Values start at 0, increasing from the left" />
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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203 <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
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204 </when>
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205 <when value="offsets_percent">
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206 <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
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207 <param name="right_column_offset" type="float" min="0" max="100" value="0" label="Offset from 3' end" />
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208 </when>
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209 </conditional>
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210 <param name="keep_zero_length" type="boolean" truevalue="keep_zero_length" falsevalue="exclude_zero_length" checked="false" label="Keep reads with zero length" />
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211 </when>
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212 <when value="dna_to_rna" />
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213 <when value="rna_to_dna" />
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214 <when value="translate">
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215 <param name="from" type="text" value="" label="From" />
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216 <param name="to" type="text" value="" label="To" />
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217 </when>
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218 <when value="change_adapter">
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219 <param name="new_adapter" type="text" value="G" label="New adapter" help="An empty string will remove the adapter base" />
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220 </when>
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221 </conditional>
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222 </when>
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223 <when value="quality">
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224 <conditional name="manipulation">
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225 <param name="manipulation_selector" type="select" label="Quality Manipulation Type">
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226 <option value="translate">String Translate</option>
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227 <!-- <option value="modify_each_score">Apply Transformation to each Score</option> Not enabled yet-->
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228 </param>
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229 <when value="translate">
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230 <param name="from" type="text" value="" label="From" />
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231 <param name="to" type="text" value="" label="To" />
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232 </when>
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233 <!-- <when value="modify_each_score">
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234 <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
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235 </when> -->
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236 </conditional>
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237 </when>
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238 <when value="miscellaneous">
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239 <conditional name="manipulation">
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240 <param name="manipulation_selector" type="select" label="Miscellaneous Manipulation Type">
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241 <option value="remove">Remove Read</option>
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242 </param>
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243 <when value="remove" />
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244 </conditional>
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245 </when>
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246 </conditional>
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247 </repeat>
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248 </inputs>
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249 <outputs>
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250 <data name="output_file" format_source="input_file" />
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251 </outputs>
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252 <tests>
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253 <!-- match all and do nothing -->
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254 <test>
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255 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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256 <param name="match_type_selector" value="identifier" />
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257 <param name="match_selector" value="regex" />
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258 <param name="match_by" value=".*" />
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259 <param name="manipulation_type_selector" value="identifier" />
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260 <param name="manipulation_selector" value="translate" />
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261 <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
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262 <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
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263 <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
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264 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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265 <!-- 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
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266 <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
267 <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
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268 <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
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269 <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
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270 <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
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271 <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
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diff changeset
272 <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
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273 <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
274 <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
275 <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
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276 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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diff changeset
277 <!-- 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
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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 <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
280 <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
281 <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
282 <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
283 <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
284 <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
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285 <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
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286 </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
287 <!-- 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
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 <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
290 <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
291 <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
292 <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
293 <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
294 <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
295 <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
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diff changeset
296 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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diff changeset
297 <!-- 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
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parents: 1
diff changeset
298 <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
299 <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
300 <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
301 <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
302 <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
303 <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
304 <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
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parents: 1
diff changeset
305 <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
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diff changeset
306 <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
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diff changeset
307 <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
308 <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
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diff changeset
309 <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
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diff changeset
310 </test>
4ac14b275aca planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit f2582539542b33240234e8ea6093e25d0aee9b6a
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diff changeset
311 <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
312 <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
313 <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
314 <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
315 <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
316 <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
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317 <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
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318 <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
319 <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
320 <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
321 <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
322 <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
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diff changeset
323 </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
324 <!-- 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
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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 <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
327 <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
328 <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
329 <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
330 <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
331 <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
332 <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
333 </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
334 <!-- 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
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 <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
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diff changeset
337 <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
338 <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
339 <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
340 <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
341 <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
342 <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
343 </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
344 <!-- 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
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 <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
347 <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
348 <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
349 <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
350 <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
351 <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
352 <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
353 </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
354 <!-- 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
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 <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
357 <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
358 <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
359 <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
360 <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
361 <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
362 <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
363 </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
364 <!-- 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
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 <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
367 <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
368 <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
369 <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
370 <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
371 <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
372 <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
373 </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
374 <!-- 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
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 <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
377 <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
378 <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
379 <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
380 <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
381 <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
382 <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
383 </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
384 <!-- 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
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 <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
387 <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
388 <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
389 <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
390 <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
391 <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
392 <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
393 </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
394 <!-- 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
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 <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
397 <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
398 <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
399 <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
400 <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
401 <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
402 <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
403 </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
404 <!-- 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
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 <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
407 <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
408 <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
409 <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
410 <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
411 <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
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412 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
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413 </test>
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414 </tests>
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415 <help><![CDATA[
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416 This tool allows you to build complex manipulations to be applied to each matching read in a FASTQ file. A read must match all matching directives in order for it to be manipulated; if a read does not match, it is output in a non-modified manner. All reads matching will have each of the specified manipulations performed upon them, in the order specified.
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417
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418 Regular Expression Matches are made using re.search, see http://docs.python.org/library/re.html for more information.
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419 All matching is performed on a single line string, regardless if e.g. the sequence or quality score spans multiple lines in the original file.
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420
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421 String translations are performed using string.translate, see http://docs.python.org/library/string.html#string.translate and http://docs.python.org/library/string.html#string.maketrans for more information.
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422
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423 .. class:: warningmark
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424
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425 Only color space reads can have adapter bases substituted.
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426
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427 -----
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428
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429 **Example**
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430
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431 Suppose you have a color space sanger formatted sequence (fastqcssanger) and you want to double-encode the color space into psuedo-nucleotide space (this is different from converting) to allow these reads to be used in tools which do not natively support it (using specially designed indexes). This tool can handle this manipulation, however, this is generally not recommended as results tend to be poorer than those produced from tools which are specially designed to handle color space data.
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432
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433 Steps:
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434
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435 1. Click **Add new Match Reads** and leave the matching options set to the default (Matching by sequence name/identifier using the regular expression "\*."; thereby matching all reads).
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436 2. Click **Add new Manipulate Reads**, change **Manipulate Reads on** to "Sequence Content", set **Sequence Manipulation Type** to "Change Adapter Base" and set **New Adapter** to "" (an empty text field).
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437 3. Click **Add new Manipulate Reads**, change **Manipulate Reads on** to "Sequence Content", set **Sequence Manipulation Type** to "String Translate" and set **From** to "0123." and **To** to "ACGTN".
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438 4. Click Execute. The new history item will contained double-encoded psuedo-nucleotide space reads.
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439 ]]></help>
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440 <citations>
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441 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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442 </citations>
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443 </tool>