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annotate sortmerna.xml @ 11:b8ba70feb088 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit f612dbbae7f8347555e561d8a09664296ce96b76-dirty
author bebatut
date Fri, 06 Nov 2015 04:40:46 -0500
parents 20b1841a740d
children bf5dbe8f7d4c
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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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22
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23 #if str( $databases.databases_selector ) == 'history'
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24 #for $db in $databases.databases_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.databases_input.input.options.tool_data_table.data])
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31 #for $db in $databases.databases_input.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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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
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44 --aligned aligned
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45
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46 $fastx.fastx_test
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47 #if $fastx.fastx_test == '--fastx'
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48 #if $fastx.fastx_rejected
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49 --other other_file
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50 #end if
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51 #end if
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52
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53 $sam.sam_test
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54 #if $sam.sam_test == '--sam'
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55 $sam.sam_sq_tag
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56 #end if
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57
6
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58 $blast_format
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59
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60 $log
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61
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62 #if $report.report_type == 'best'
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63 #if $report.report_best.report_best_type == '0'
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64 --best 0
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65 #else if $report.report_best.report_best_type == '1'
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66 --best 1
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67 --min_lis $report.report_best.report_best_min_lis
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68 #else
6
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69 --best $report.report_best.report_best_value
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70 --min_list $report.report_best.report_best_min_lis
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71 #end if
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72 #else
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73 #if $report.report_num_alignments.report_num_alignments_type == '0'
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74 --num_alignments 0
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75 #else if $report.report_num_alignments.report_num_alignments_type == '1'
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76 --num_alignments 1
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77 #else
6
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78 --num_alignments $report.report_num_alignments.report_num_alignments_value
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79 #end if
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80 #end if
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81
2
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82 -e $e_value
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83 --match $match
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84 --mismatch $mismatch
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85 --gap_open $gap_open
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86 --gap_ext $gap_ext
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87 -N $ambiguous_letter
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88
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89 #if $strand == 'forward'
0
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90 -F
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91 #end if
6
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92 #if $strand == 'reverse'
0
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93 -R
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94 #end if
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95 ]]>
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96 </command>
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97
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98 <inputs>
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99 <param name="input_sequence_file" type="data" format="fastq,fasta" label="Input sequence file" help=""/>
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100
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101 <conditional name="databases">
0
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102 <param name="databases_selector" type="select" label="Databases to query" help="">
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103 <option value="cached" selected="true">Public ribosomal databases</option>
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104 <option value="history">Databases from your history</option>
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105 </param>
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106 <when value="cached">
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107 <param name="databases_input" label="rRNA databases" type="select" display="checkboxes" multiple="true">
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108 <options from_data_table="sortmerna_rRNA_databases" />
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109 <validator type="no_options" message="Select at least one database"/>
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110 </param>
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111 </when>
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112 <when value="history">
6
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113 <param name="databases_name" type="data" format="fasta" multiple="true" label="rRNA databases"
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114 help=""/>
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115 </when>
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116 </conditional>
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117
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118 <conditional name="fastx">
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119 <param name="fastx_test" type='select' label="Output into Fasta/FastQ file?" help="">
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120 <option value="--fastx">Yes</option>
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121 <option value="">No</option>
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122 </param>
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123 <when value="--fastx">
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124 <param name='fastx_rejected' type='boolean' checked="true" label="Conserve rejected reads?" help=""/>
0
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125 </when>
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126 </conditional>
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127
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128 <conditional name="sam">
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129 <param name="sam_test" type='select' label="Output SAM alignments?" help="">
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130 <option value="--sam">Yes</option>
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131 <option value="">No</option>
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132 </param>
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133 <when value="--sam">
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134 <param name='sam_sq_tag' type='boolean' checked="true" truevalue="--SQ" falsevalue="" label="Add SQ tags to SAM file?" help=""/>
0
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135 </when>
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136 </conditional>
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137
6
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138 <param name="blast_format" type="select" display="radio" label="Format for BLAST output" help="">
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139 <option value="--blast 0">Pairwise</option>
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140 <option value="--blast 1">Tabular (Blast -m 8 format)</option>
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141 <option value="--blast 2'">Tabular + column for CIGAR</option>
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142 <option value="--blast 3" selected="true">Tabular + columns for CIGAR and query coverage</option>
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143 <option value="">No Blast output</option>
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144 </param>
0
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145
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146 <param name='log' type='boolean' checked="true" truevalue="--log" falsevalue="" label="Conserve overall statistic output into a log file?" help=""/>
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147
0
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148 <conditional name="report">
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149 <param name="report_type" type="select" display="radio" label="Parameters for filtering and read mapping" help="">
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150 <option value="best" selected="true">Report best alignments per read reaching E-value</option>
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151 <option value="num_alignments">Report first alignements per read reaching E-value</option>
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152 </param>
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153 <when value="best">
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154 <conditional name="report_best">
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155 <param name="report_best_type" type="select" display="radio" label="Number of searched alignments" help="Only the best alignment is reported">
0
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156 <option value="0">All high-candidate reference sequences are searched for alignments (very slow)</option>
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157 <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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158 <option value="other_value">A custom number of reference sequences are searched for alignments (speed decrease for high value)</option>
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159 </param>
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160 <when value="other_value">
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161 <param name="report_best_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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162 <param name="report_best_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."/>
0
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163 </when>
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164 <when value="1">
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165 <param name="report_best_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."/>
0
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166 </when>
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167 </conditional>
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168 </when>
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169 <when value="num_alignments">
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170 <conditional name="report_num_alignments">
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171 <param name="report_num_alignments_type" type="select" display="radio" label="Number of output alignments" help="">
0
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172 <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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173 <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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174 <option value="other_value">A custom number of alignments are made and reported (speed decrease for high value)</option>
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175 </param>
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176 <when value="other_value">
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177 <param name="report_num_alignments_value" type="integer" min="0" max="100" value="1" label="Number of alignments to be made and reported" help=""/>
0
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178 </when>
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179 </conditional>
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180 </when>
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181 </conditional>
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182
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183 <param name="e_value" type="float" min="0" max="10" value="1" label="E-value threshold" help=""/>
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184 <param name="match" type="integer" min="0" max="10" value="2" label="SW score for a match" help=""/>
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185 <param name="mismatch" type="integer" min="-10" max="0" value="-3" label="SW penalty for a mismatch" help=""/>
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186 <param name="gap_open" type="integer" min="0" max="10" value="5" label="SW penalty for introducing a gap" help=""/>
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187 <param name="gap_ext" type="integer" min="0" max="10" value="2" label="SW penalty for extending a gap" help=""/>
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188 <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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189
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190 <param name="strand" type="select" display="radio" label="Search on" help="">
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191 <option value="both" selected="true">Both strands</option>
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192 <option value="forward" >Only forward strand</option>
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193 <option value="reverse" >Only reverse-complementary strand</option>
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194 </param>
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195
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196 <param name="seed_length" type="integer" min="0" max="100" value="18" label="Seed length for database indexing" help=""/>
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197 <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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198 </inputs>
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199
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200 <outputs>
5
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201 <data format_source="input_sequence_file" name="aligned_sequence_file"
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202 metadata="input_sequence_file" from_work_dir="aligned.dat"
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203 label="Aligned sequences on ${on_string} (SortMeRNA)">
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204 <filter>((fastx['fastx_test']))</filter>
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205 </data>
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206
5
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207 <data format_source="input_sequence_file" name="rejected_sequence_file"
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208 metadata="input_sequence_file" from_work_dir="other_file.dat"
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209 label="Rejected sequences on ${on_string} (SortMeRNA)">
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210 <filter>((fastx['fastx_test'] and fastx['fastx_rejected']))</filter>
0
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211 </data>
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212
5
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213 <data format="sam" name="sam_alignment_file" metadata="input_sequence_file"
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214 from_work_dir="aligned.sam"
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215 label="SAM alignments on ${on_string} (SortMeRNA)">
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216 <filter>((sam['sam_test']]))</filter>
0
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217 </data>
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218
5
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219 <data format="tabular" name="blast_output_file"
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220 metadata="input_sequence_file" from_work_dir="aligned.blast"
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221 label="Blast alignments on ${on_string} (SortMeRNA)">
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222 <filter>blast_format</filter>
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223 <change_format>
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224 <when input="blast_format" value="--blast 0" format="txt" />
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225 </change_format>
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226 </data>
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227
5
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228 <data format="txt" name="output_log" metadata="input_sequence_file"
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229 from_work_dir="aligned.log" label="Log on ${on_string} (SortMeRNA)">
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230 <filter>log</filter>
0
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231 </data>
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232 </outputs>
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233
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234 <tests>
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235 <test>
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236 <param name="input_sequence_file" value="input_sequences.fastq" ftype="fastq"/>
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237 <param name="databases_selector" value="history" />
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238 <param name="databases_name" value="db.fasta" ftype="fasta"/>
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239 <param name="fastx_test" value="--fastx" />
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240 <param name='fastx_rejected' value="True"/>
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241 <param name="sam_test" value="" />
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242 <param name="blast_format" value="--blast 3" />
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243 <param name='log' value="" />
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244 <param name="report_type" value="best" />
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245 <param name="report_best_type" value="1" />
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246 <param name="report_best_min_lis" value="2" />
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247 <param name="e_value" value="1" />
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248 <param name="match" value="2" />
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249 <param name="mismatch" value="-3" />
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250 <param name="gap_open" value="5" />
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251 <param name="gap_ext" value="2" />
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252 <param name="ambiguous_letter" value="-3" />
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253 <param name="strand" value="both" />
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254 <param name="seed_length" value="18" />
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255 <param name="max_pos" value="10000" />
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256
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257 <output name="aligned_sequence_file" file="aligned_sequences.fastq" ftype="fastq"/>
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258 <output name="rejected_sequence_file" file="rejected_sequences.fastq" ftype="fastq"/>
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259 <output name="blast_output_file" file="blast_output.tabular" ftype="tabular"/>
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260 </test>
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261 </tests>
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262
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263 <help><![CDATA[
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264
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265 **What it does**
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266
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267 SortMeRNA is a tool for RNA filtering based on local sequence alignment against
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268 rRNA database. For more information, check the `user manual <http://bioinfo.lifl.fr/RNA/sortmerna/code/SortMeRNA-user-manual-v1.7.pdf>`_.
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269
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270 -----
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271
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272 **Input**
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273
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274 The input is a sequence file in fasta or fastq and databases to search against.
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275 These databases have to be indexed before the sequence alignment.
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276
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277 SortMeRNA is distributed with 8 rRNA databases constructed from SILVA SSU,LSU
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278 (version 111) and the RFAM 5/5.8S (version 11.0) databases:
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279
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280 - SILVA 16S bacteria
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281 - SILVA 16S archaea
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282 - SILVA 18S eukarya
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283 - SILVA 23S bacteria
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284 - SILVA 23s archaea
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285 - SILVA 28S eukarya
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286 - Rfam 5S archaea/bacteria
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287 - Rfam 5.8S eukarya
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288
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289 These databases are available as public ribosomal databases. But local databases
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290 can also be used.
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291
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292 -----
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293
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294 **Parameters**
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295
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296 The database index can be modulated by:
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297
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298 - Seed length
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299 - Maximum number of positions to store for each k-mer for database indexing
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300
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301 For RNA sorting, the parameters are:
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302
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303 - Test to output files in fasta or fastq, in sam and/or in blast format
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304 - Test for conservation of rejected sequences
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305 - Choice in blast format
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306 - Test to add SQ tags in sam file
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307 - Filtering and read mapping parameters
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308 - Test for conservation of best alignment or first alignment
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309 - Number of searched, conserved alignments
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310 - E-value threshold
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311 - SW score for a match, for a mismatch, for introducing a gap, for extending a gap, for ambigous letters
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312 - Strand to search
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313
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314 -----
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315
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316 **Outputs**
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317
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318 Given the choosen parameters, several outputs are possible
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319
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320 - Sequence file in fasta or fastq with aligned sequences (or conserved)
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321 - Sequence file in fasta or fastq with rejected sequences
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322 - File with sam alignments
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323 - File with blast outputs
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325
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326 ]]></help>
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327
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328 <citations>
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329 <citation type="doi">10.1093/bioinformatics/bts611</citation>
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330 </citations>
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331 </tool>