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annotate sortmerna.xml @ 0:a8ac09e937f3 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
author rnateam
date Mon, 03 Aug 2015 08:18:26 -0400
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a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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1 <tool id="bg_sortmerna" name="Filter with SortMeRNA" version="1.9.0">
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2 <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description>
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3 <requirements>
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4 <requirement type='package' version="1.9">sortmerna</requirement>
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5 </requirements>
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6 <stdio>
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7 <regex match="This program builds a Burst trie on an input rRNA database"
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8 source="both"
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9 level="fatal"
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10 description="Buildtrie program failed to execute." />
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11 <regex match="The database name"
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12 source="both"
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13 level="fatal"
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14 description="The database ${databases} has not been preprocessed using buildtrie before using SortMeRNA." />
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15 </stdio>
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16 <version_command>
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17 <![CDATA[
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18 sortmerna --version 2>&1|grep 'SortMeRNA version'
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19 ]]>
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20 </version_command>
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21 <command interpreter="python">
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22 <![CDATA[
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23 sortmerna.py
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24 --sortmerna "
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25 $strand_search
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26 #if str( $read_family.read_family_selector ) == 'other':
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27 --I $input_reads -r $read_family.ratio_parameter
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28 #else:
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29 $read_family.read_family_selector $input_reads
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30 #end if
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31
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32 #if str( $sequencing_type.sequencing_type_selector ) == 'paired':
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33 $sequencing_type.paired_type
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34 #end if
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35
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36 #if $outputs_selected:
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37 #if 'accept' in $outputs_selected.value:
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38 --accept accept_file
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39 #end if
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40 #if 'other' in $outputs_selected.value:
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41 --other other_file
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42 #end if
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43 #end if
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44
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45 $log
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46 -a \${GALAXY_SLOTS:-4}
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47 "
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48 #if str( $databases_type.databases_selector ) == 'history':
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49 --buildtrie
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50 #for $db in $databases_type.input_databases
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51 $db.database_name
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52 #end for
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53 #else:
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54 ## databases path is not directly accessible, must match by hand with LOC file contents
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55 ${' '.join([dict([(x[0], x[2]) for x in $databases_type.input_databases.input.options.tool_data_table.data])[y]
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56 for y in $databases_type.input_databases.value])}
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57 #end if
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58 ]]>
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59 </command>
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60 <inputs>
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61 <conditional name="read_family">
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62 <param name="read_family_selector" type="select" format="text" label="Sequencing technology of querying sequences (reads)"
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63 help="The Illumina platform is more common for large scale metatranscriptomic projects requiring a high throughput.">
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64 <option value="--I">Illumina Solexa</option>
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65 <option value="--454">454 Roche</option>
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66 <option value="other">Other</option>
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67 </param>
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68 <when value="other">
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69 <param name="ratio_parameter" type="float" value="1" min="0" max="1"
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70 label="Ratio parameter (the number of hits on the read / read length)"
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71 help="The ratio parameter for SortMeRNA has been set to r=0.25 for Illumina Solexa reads and to r=0.15 for 454 Roche reads.
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72 For other read types, if the sequencing technology produces high quality reads with a low substitution error rate
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73 (0.1 substitutions per 100 bases, such as Illumina), then the ratio parameter can be set to r=[0.23,0.27].
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74 If the sequencing technology has a high indel error rate (1-2 indels per 100 bases, such as 454 or Ion Torrent),
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75 then the ratio parameter can be set to r=[0.13,0.17] (-r)."/>
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76 </when>
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77 </conditional>
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78 <param format="fasta,fastq" name="input_reads" type="data" label="Querying sequences (reads)" help=""/>
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79 <conditional name="sequencing_type">
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80 <param name="sequencing_type_selector" type="select" label="Sequencing type">
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81 <option value="not_paired">Reads are not paired</option>
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82 <option value="paired">Reads are paired</option>
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83 </param>
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84 <when value="paired">
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85 <param name="paired_type" type="select" display="radio" label="If one read of a pair is accepted and the other not, output both reads"
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86 help="SortMeRNA does not use the pairing information for filtering RNA,
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87 however if one read of a pair is accepted and the other is not,
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88 the resulting output may break apart the pair into two separate files.
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89 The purpose of 'Reads are paired' option is to preserve the pairing of the reads.">
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90 <option value="--paired-in">to accepted file (--paired-in)</option>
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91 <option value="--paired-out">to rejected file (--paired-out)</option>
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92 </param>
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93 </when>
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94 </conditional>
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95
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96 <param name="strand_search" type="select" label="Which strands to search" display="radio">
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97 <option value="">Search both strands</option>
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98 <option value="-F">Search only the forward strand (-F)</option>
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99 <option value="-R">Search only the reverse-complementary strand (-R)</option>
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100 </param>
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101
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102 <conditional name="databases_type">
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103 <param name="databases_selector" type="select" label="Databases to query"
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104 help="Public rRNA databases provided with SortMeRNA have been indexed.
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105 On the contrary, personal databases must be indexed each time SortMeRNA is launched.
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106 Please be patient, this may take some time depending on the size of the given database.">
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107 <option value="cached" selected="true">Public ribosomal databases</option>
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108 <option value="history">Databases from your history</option>
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109 </param>
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110 <when value="cached">
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111 <param name="input_databases" label="rRNA database" type="select" display="checkboxes" multiple="true">
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112 <options from_data_table="rRNA_databases" />
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113 <validator type="no_options" message="Select at least one database"/>
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114 </param>
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115 </when>
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116 <when value="history">
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117 <repeat name="input_databases" title="Database" min="1">
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118 <param name="database_name" type="data" format="fasta" label="rRNA database"
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119 help="Your database will be indexed first, which may take up to several minutes."/>
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120 </repeat>
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121 </when>
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122 </conditional>
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123
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124 <!-- Outputs -->
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125 <param name="outputs_selected" type="select" display="checkboxes" multiple="true" label="Output options">
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126 <option value="accept" selected="True">Reads matching to at least one database</option>
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127 <option value="other">Reads not found in any database</option>
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128 </param>
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129 <param name="log" type="boolean" checked="False" truevalue="--log log_file" falsevalue="" label="Statistics file"
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130 help="Generates statistics for the rRNA content of reads, as well as rRNA subunit distribution. (--log)">
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131 </param>
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132
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133 </inputs>
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134 <outputs>
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135 <data format_source="input_reads" name="output_accept" from_work_dir="accept_file.dat"
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136 label="Matching reads on ${on_string} (${input_reads.datatype.file_ext})">
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137 <filter>outputs_selected and 'accept' in outputs_selected</filter>
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138 </data>
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139 <data format_source="input_reads" name="output_other" from_work_dir="other_file.dat"
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140 label="Reads not found on ${on_string} (${input_reads.datatype.file_ext})">
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141 <filter>outputs_selected and 'other' in outputs_selected</filter>
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142 </data>
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143 <data format="txt" name="output_log" label="${tool.name} statistics (txt)" from_work_dir="log_file.log">
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144 <filter>log</filter>
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145 </data>
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146 </outputs>
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147 <tests>
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148 <test>
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149 <param name="read_family_selector" value="I" />
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150 <param name="input_reads" value="sortmerna_wrapper_in1.fastq" />
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151 <param name="sequencing_type_selector" value="not_paired" />
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152 <param name="strand_search" value="" />
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153 <param name="databases_selector" value="cached" />
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154 <param name="input_databases" value="rfam-5.8s,rfam-5s" />
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155 <param name="outputs_selected" value="accept,other" />
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156 <param name="log" value="" />
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157 <param name="options_type_selector" value="less" />
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158 <output name="output_accept" file="sortmerna_wrapper_accept1.fastq" />
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159 <output name="output_other" file="sortmerna_wrapper_other1.fastq" />
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160 </test>
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161 </tests>
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162 <help>
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163 <![CDATA[
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164 **What it does**
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165
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166 SortMeRNA_ is a software designed to rapidly filter ribosomal RNA fragments
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167 from metatransriptomic data produced by next-generation sequencers.
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168 It is capable of handling large RNA databases and sorting out all fragments
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169 matching to the database with high accuracy and specificity.
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170
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171 .. _SortMeRNA: http://bioinfo.lifl.fr/RNA/sortmerna/
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172
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173
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174 **Input**
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175
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176 The input is one file of reads in FASTA or FASTQ format and any number of rRNA databases to search against.
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177 If the user has two foward-reverse paired-sequencing reads files, they may use
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178 the script "merge_paired_reads.sh" to interleave the reads into one file, preserving their order.
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179
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180 If the sequencing type for the reads is paired-ended, the user has two options under
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181 "Sequencing type" to filter the reads and preserve their order in the file.
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182 For a further example of each option, please refer to Section 4.2.3 in the `SortMeRNA User Manual`_.
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183
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184 .. _sortmerna user manual: http://bioinfo.lifl.fr/RNA/sortmerna/code/SortMeRNA-user-manual-v1.7.pdf
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185
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186
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187 **Output**
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188
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189 The output will follow the same format (FASTA or FASTQ) as the reads. Optionally, a statistic file for the rRNA content of reads, as well as rRNA subunit distribution can be generated.
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190
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191
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192 **rRNA databases**
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193
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194 SortMeRNA is distributed with 8 representative rRNA databases, which were
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195 all constructed from the SILVA SSU,LSU (version 111) and the RFAM 5/5.8S
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196 (version 11.0) databases using the tool UCLUST.
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197
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198 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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199 | Representative database | id % | average id% | # seq (clustered) | Origin | # seq (original) |
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200 +==========================+======+=============+===================+========================+===================+
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201 | SILVA 16S bacteria | 85 | 91.6 | 8174 | SILVA SSU Ref NR v.111 | 244077 |
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202 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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203 | SILVA 16S archaea | 95 | 96.7 | 3845 | SILVA SSU Ref NR v.111 | 10919 |
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204 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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205 | SILVA 18S eukarya | 95 | 96.7 | 4512 | SILVA SSU Ref NR v.111 | 31862 |
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206 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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207 | SILVA 23S bacteria | 98 | 99.4 | 3055 | SILVA LSU Ref v.111 | 19580 |
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208 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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209 | SILVA 23s archaea | 98 | 99.5 | 164 | SILVA LSU Ref v.111 | 405 |
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210 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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211 | SILVA 28S eukarya | 98 | 99.1 | 4578 | SILVA LSU Ref v.111 | 9321 |
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212 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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213 | Rfam 5S archaea/bacteria | 98 | 99.2 | 59513 | RFAM | 116760 |
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214 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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215 | Rfam 5.8S eukarya | 98 | 98.9 | 13034 | RFAM | 225185 |
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216 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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217
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218 id %: members of the cluster must have identity at least 'id %' identity with the representative sequence
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219
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220 average id %: average identity of a cluster member to the representative sequence
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221
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222 The user may also choose to use their own rRNA databases.
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223
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224 .. class:: warningmark
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225
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226 Note that your personal databases are indexed each time, and that
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227 this may take some time depending on the size of the given database.
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228 ]]>
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229 </help>
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230
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231 <citations>
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232 <citation type="doi">10.1093/bioinformatics/bts611</citation>
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233 <citation type="doi">10.1093/nar/gks1219</citation>
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234 <citation type="doi">10.1093/nar/gks1005</citation>
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235 <citation type="doi">10.1093/bioinformatics/btq461</citation>
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236 <citation type="doi">10.1038/nbt.2198</citation>
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237 </citations>
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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238 </tool>