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annotate sortmerna.xml @ 5:064dbe9f9333 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 4d9df680f128bc18183ebba6f85fc24f11207571-dirty
author bebatut
date Wed, 28 Oct 2015 08:36:01 -0400
parents 5d7ec21f6d4c
children 817fb14fc739
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1 <tool id="sortmerna" name="SortMeRNA" version="0.1.0">
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2 <description>to filter ribosomal RNAs in metatranscriptomic data</description>
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3
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4 <requirements>
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5 <requirement type="package" version="2.0">sortmerna</requirement>
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6 </requirements>
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7
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8 <stdio>
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9 <exit_code range="1:" />
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10 </stdio>
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11
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12 <version_command>
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13 <![CDATA[
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14 sortmerna --version 2>&1|grep 'SortMeRNA version'
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15 ]]>
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16 </version_command>
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18 <command>
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19 <![CDATA[
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20 #set $ref = ''
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21 #set $sep=''
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23 #if str( $databases_type.databases_selector ) == 'history':
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24 #for $db in $databases_type.database_name
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25 #set $ref += $sep + str($db) + ',' + $os.path.splitext($os.path.basename(str($db)))[0]
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26 #set $sep = ':'
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27 #end for
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28 #else:
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29 ## databases path is not directly accessible, must match by hand with LOC file contents
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30 #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data])
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31 #for $db in $databases_type.input_databases.value
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32 #set $ref += $sep + $data_table[$db] + ',' + $os.path.splitext($data_table[$db])[0]
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33 #set $sep = ':'
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34 #end for
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35 #end if
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36
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37 indexdb_rna --ref $ref -L $seed_length --max_pos $max_pos
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38
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39 &&
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41 sortmerna
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42 --ref $ref
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43 --reads $input_sequence_file
3
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44 --aligned aligned
0
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45
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46 #if $fastx.test:
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47 --fastx
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48 #if $fastx.rejected:
3
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49 --other other_file
0
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50 #end if
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51 #end if
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52
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53 #if $sam.test:
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54 --sam
1
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55 $sam.sq_tag
0
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56 #end if
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57
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58 #if $blast.test:
3
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59 --blast "$blast.format"
0
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60 #end if
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61
4
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62 $log
3
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63
0
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64 #if $report.type == 'best':
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65 #if $report.best.type == '0':
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66 --best 0
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67 #else if $report.best.type == '1':
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68 --best 1
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69 --min_lis $report.best.min_lis
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70 #else
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71 --best $report.best.value
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72 --min_list $report.best.min_lis
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73 #end if
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74 #else
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75 #if $report.num_alignments.type == '0':
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76 --num_alignments 0
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77 #else if $report.num_alignments.type == '1':
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78 --num_alignments 1
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79 #else
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80 --num_alignments $report.num_alignments.value
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81 #end if
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82 #end if
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83
2
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84 -e $e_value
0
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85 --match $match
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86 --mismatch $mismatch
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87 --gap_open $gap_open
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88 --gap_ext $gap_ext
2
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89 -N $ambiguous_letter
0
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90
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91 #if $strand == 'forward':
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92 -F
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93 #end if
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94 #if $strand == 'reverse':
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95 -R
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96 #end if
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97 ]]>
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98 </command>
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99
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100 <inputs>
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101 <param name="input_sequence_file" type="data" format="fastq,fasta" label="Input sequence file" help=""/>
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102
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103 <conditional name="databases_type">
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104 <param name="databases_selector" type="select" label="Databases to query" help="">
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105 <option value="cached" selected="true">Public ribosomal databases</option>
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106 <option value="history">Databases from your history</option>
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107 </param>
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108 <when value="cached">
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109 <param name="input_databases" label="rRNA databases" type="select" display="checkboxes" multiple="true">
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110 <options from_data_table="sortmerna_rRNA_databases" />
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111 <validator type="no_options" message="Select at least one database"/>
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112 </param>
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113 </when>
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114 <when value="history">
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115 <param name="database_name" type="data" format="fasta" multiple="true" label="rRNA databases"
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116 help=""/>
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117 </when>
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118 </conditional>
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119
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120 <conditional name="fastx">
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121 <param name="test" type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Output into Fasta/FastQ file?" help="" />
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122 <when value="yes">
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123 <param name='rejected' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Conserve rejected reads?" help=""/>
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124 </when>
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125 </conditional>
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126
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127 <conditional name="sam">
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128 <param name="test" type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Output SAM alignments?" help="" />
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129 <when value="yes">
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130 <param name='sq_tag' type='boolean' checked="true" truevalue='--SQ' falsevalue='' label="Add SQ tags to SAM file?" help=""/>
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131 </when>
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132 </conditional>
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133
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134 <conditional name="blast">
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135 <param name='test' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Output BLAST alignments?" help=""/>
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136 <when value="yes">
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137 <param name="format" type="select" display="radio" label="Format for BLAST output" help="">
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138 <option value="0">Pairwise</option>
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139 <option value="1">Tabular (Blast -m 8 format)</option>
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140 <option value="1 cigar">Tabular + column for CIGAR</option>
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141 <option value="1 cigar qcov" selected="true">Tabular + columns for CIGAR and query coverage</option>
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142 <option value="1 cigar qcov qstrand">Tabular + columns for CIGAR, query coverage and strand</option>
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143 </param>
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144 </when>
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145 </conditional>
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146
4
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147 <param name='log' type='boolean' checked="true" truevalue='--log' falsevalue='' label="Conserve overall statistic output into a log file?" help=""/>
3
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148
0
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149 <conditional name="report">
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150 <param name="type" type="select" display="radio" label="Parameters for filtering and read mapping" help="">
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151 <option value="best" selected="true">Report best alignments per read reaching E-value</option>
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152 <option value="num_alignments">Report first alignements per read reaching E-value</option>
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153 </param>
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154 <when value="best">
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155 <conditional name="best">
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156 <param name="type" type="select" display="radio" label="Number of searched alignments" help="Only the best alignment is reported">
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157 <option value="0">All high-candidate reference sequences are searched for alignments (very slow)</option>
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158 <option value="1" selected="true">Only one high-candidate reference sequence is searched for alignments (fast). The high-candidate sequences are determined heuristically using a LIS of seed matches)</option>
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159 <option value="other_value">A custom number of reference sequences are searched for alignments (speed decrease for high value)</option>
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160 </param>
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161 <when value="other_value">
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162 <param name="value" type="integer" min="0" max="100" value="1" label="Number of alignments to be made" help="Only the best one is reported. The computation speed decrease with high value"/>
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163 <param name="min_lis" type="integer" min="0" max="100" value="2" label="Number of longest LIS an alignement needs to be searched" help="The alignements having the first INT longest LIS. LIS stands for Longest Increasing Subsequence, it is computed using seeds' positions to expand hits into longer matches prior to Smith-Waterman alignment."/>
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164 </when>
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165 <when value="1">
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166 <param name="min_lis" type="integer" min="0" max="100" value="2" label="Number of longest LIS an alignement needs to be searched" help="The alignements having the first INT longest LIS. LIS stands for Longest Increasing Subsequence, it is computed using seeds' positions to expand hits into longer matches prior to Smith-Waterman alignment."/>
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167 </when>
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168 </conditional>
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169 </when>
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170 <when value="num_alignments">
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171 <conditional name="num_alignments">
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172 <param name="type" type="select" display="radio" label="Number of output alignments" help="">
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173 <option value="0">All alignments reaching the E-value threshold are reported (very slow, this option is not suggested for high similarity rRNA databases)</option>
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174 <option value="1" selected="true">The first alignment passing E-value threshold are reported (very fast, best choice if only filtering is needed)</option>
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175 <option value="other_value">A custom number of alignments are made and reported (speed decrease for high value)</option>
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176 </param>
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177 <when value="other_value">
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178 <param name="value" type="integer" min="0" max="100" value="1" label="Number of alignments to be made and reported" help=""/>
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179 </when>
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180 </conditional>
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181 </when>
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182 </conditional>
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183
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184 <param name="e_value" type="float" min="0" max="10" value="1" label="E-value threshold" help=""/>
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185 <param name="match" type="integer" min="0" max="10" value="2" label="SW score for a match" help=""/>
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186 <param name="mismatch" type="integer" min="-10" max="0" value="-3" label="SW penalty for a mismatch" help=""/>
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187 <param name="gap_open" type="integer" min="0" max="10" value="5" label="SW penalty for introducing a gap" help=""/>
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188 <param name="gap_ext" type="integer" min="0" max="10" value="2" label="SW penalty for extending a gap" help=""/>
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189 <param name="ambiguous_letter" type="integer" min="-10" max="0" value="-3" label="SW penalty for ambiguous letters (N's)" help=""/>
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190
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191 <param name="strand" type="select" display="radio" label="Search on" help="">
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192 <option value="both" selected="true">Both strands</option>
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193 <option value="forward" >Only forward strand</option>
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194 <option value="reverse" >Only reverse-complementary strand</option>
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195 </param>
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196
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197 <param name="seed_length" type="integer" min="0" max="100" value="18" label="Seed length for database indexing" help=""/>
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198 <param name="max_pos" type="integer" min="0" max="100000" value="10000" label="Maximum number of positions to store for each k-mer for database indexing" help="With 0, all positions are stored"/>
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199 </inputs>
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200
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201 <outputs>
5
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202 <data format_source="input_sequence_file" name="aligned_sequence_file"
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203 metadata="input_sequence_file" from_work_dir="aligned.dat"
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204 label="Aligned sequences on ${on_string} (SortMeRNA)">
0
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205 <filter>((fastx['test']))</filter>
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206 </data>
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207
5
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208 <data format_source="input_sequence_file" name="rejected_sequence_file"
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209 metadata="input_sequence_file" from_work_dir="other_file.dat"
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210 label="Rejected sequences on ${on_string} (SortMeRNA)">
0
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211 <filter>((fastx['test'] and fastx['rejected']))</filter>
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212 </data>
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213
5
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214 <data format="sam" name="sam_alignment_file" metadata="input_sequence_file"
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215 from_work_dir="aligned.sam"
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216 label="SAM alignments on ${on_string} (SortMeRNA)">
0
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217 <filter>((sam['test']]))</filter>
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218 </data>
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219
5
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220 <data format="tabular" name="blast_output_file"
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221 metadata="input_sequence_file" from_work_dir="aligned.blast"
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222 label="Blast alignments on ${on_string} (SortMeRNA)">
0
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223 <filter>((blast['test']))</filter>
3
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224 <change_format>
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225 <when input="blast.format" value="0" format="txt" />
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226 </change_format>
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227 </data>
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228
5
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229 <data format="txt" name="output_log" metadata="input_sequence_file"
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230 from_work_dir="aligned.log" label="Log on ${on_string} (SortMeRNA)">
4
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231 <filter>log</filter>
0
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232 </data>
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233 </outputs>
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234
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235 <tests>
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236 <test>
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237 <param name="input_sequence_file" value="input_sequences.fastq"/>
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238 <param name="databases_selector" value="history"/>
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239 <param name="database_name" value="db.fasta"/>
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240 <param name="fastx.test" value="yes"/>
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241 <param name="fastx.rejected" value="yes"/>
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242 <param name="sam.test" value="yes"/>
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243 <param name="blast.test" value="yes"/>
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244 <param name="blast.format" value="1 cigar qcov"/>
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245 <param name="report.type" value="best"/>
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246 <param name="report.best.type" value="1"/>
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247 <param name="report.best.min_lis" value="2"/>
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248 <param name="e_value" value="1"/>
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249 <param name="match" value="2"/>
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250 <param name="mismatch" value="-3"/>
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251 <param name="gap_open" value="5" />
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252 <param name="gap_ext" value="2"/>
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253 <param name="ambiguous_letter" value="-3"/>
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254 <param name="strand" value="both"/>
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255 <param name="seed_length" value="18"/>
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256 <param name="max_pos" value="10000"/>
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257
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258 <output name="aligned_sequence_file" file="aligned_sequences.fastq"/>
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259 <output name="rejected_sequence_file" file="rejected_sequences.fastq"/>
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260 <output name="blast_output_file" file="blast_output.txt"/>
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261 <output name="sam_alignment_file" file="sam_alignments.sam"/>
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262 </test>
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263 </tests>
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264
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265 <help><![CDATA[
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266
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267 **What it does**
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268
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269 SortMeRNA is a tool for RNA filtering based on local sequence alignment against
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270 rRNA database
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271
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272 .. _sortmerna user manual: http://bioinfo.lifl.fr/RNA/sortmerna/code/SortMeRNA-user-manual-v1.7.pdf
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273
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274 -----
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275
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276 **Input**
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277
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278 The input is a sequence file in fasta or fastq and databases to search against.
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279 These databases have to be indexed before the sequence alignment.
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280
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281 SortMeRNA is distributed with 8 rRNA databases constructed from SILVA SSU,LSU
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282 (version 111) and the RFAM 5/5.8S (version 11.0) databases:
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283
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284 - SILVA 16S bacteria
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285 - SILVA 16S archaea
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286 - SILVA 18S eukarya
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287 - SILVA 23S bacteria
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288 - SILVA 23s archaea
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289 - SILVA 28S eukarya
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290 - Rfam 5S archaea/bacteria
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291 - Rfam 5.8S eukarya
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292
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293 These databases are available as public ribosomal databases. But local databases
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294 can also be used.
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295
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296 -----
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297
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298 **Parameters**
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299
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300 The database index can be modulated by:
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301
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302 - Seed length
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303 - Maximum number of positions to store for each k-mer for database indexing
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304
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305 For RNA sorting, the parameters are:
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306
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307 - Test to output files in fasta or fastq, in sam and/or in blast format
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308 - Test for conservation of rejected sequences
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309 - Choice in blast format
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310 - Test to add SQ tags in sam file
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311 - Filtering and read mapping parameters
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312 - Test for conservation of best alignment or first alignment
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313 - Number of searched, conserved alignments
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314 - E-value threshold
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315 - SW score for a match, for a mismatch, for introducing a gap, for extending
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316 a gap, for ambigous letters
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317 - Strand to search
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318
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319 -----
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320
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321 **Outputs**
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322
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323 Given the choosen parameters, several outputs are possible
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324
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325 - Sequence file in fasta or fastq with aligned sequences (or conserved)
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326 - Sequence file in fasta or fastq with rejected sequences
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327 - File with sam alignments
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328 - File with blast outputs
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329
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330
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331 ]]></help>
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332
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333 <citations>
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334 <citation type="doi">10.1093/bioinformatics/bts611</citation>
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335 </citations>
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336 </tool>