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annotate sortmerna.xml @ 1:dd73a3422870 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 8f8692e83217a072a3ed928469621f1f606ab28a-dirty
author rnateam
date Tue, 04 Aug 2015 04:17:05 -0400
parents e18696d1bc0e
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dd73a3422870 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 8f8692e83217a072a3ed928469621f1f606ab28a-dirty
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1 <tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.0.0">
0
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2 <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description>
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3 <requirements>
1
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4 <requirement type='package' version="2.0">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>
0
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22 <![CDATA[
1
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23 #set $ref = ''
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24 #set $sep=''
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25 #if str( $databases_type.databases_selector ) == 'history':
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26 #for $db in $databases_type.input_databases
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27 #set $ref += $sep + str($db.database_name) + ',' + $os.path.splitext($os.path.basename(str($db.database_name)))[0]
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28 #set $sep = ':'
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29 #end for
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30 indexdb_rna --ref $ref
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31 #else:
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32 ## databases path is not directly accessible, must match by hand with LOC file contents
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33 #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data])
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34 #for $db in $databases_type.input_databases.value
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35 #set $ref += $sep + $data_table[$db] + ',' + $os.path.splitext($data_table[$db])[0]
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36 #set $sep = ':'
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37 #end for
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38 #end if
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39 &&
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40 sortmerna --ref $ref --reads $input_reads --aligned aligned
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41 #if str( $sequencing_type.sequencing_type_selector ) == 'paired'
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42 $sequencing_type.paired_type
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43 #end if
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44 $strand_search
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45 $aligned_fastx.aligned_fastx_selector
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46 #if $aligned_fastx.aligned_fastx_selector == '--fastx'
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47 #if $aligned_fastx.other
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48 --other other_file
0
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49 #end if
1
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50 #end if
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51 $aligned_sam.aligned_sam_selector
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52 #if $aligned_sam.aligned_sam_selector == '--sam'
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53 $aligned_sam.sq
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54 #end if
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55 $aligned_blast
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56 $log
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57 -a \${GALAXY_SLOTS:-1}
0
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58 ]]>
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59 </command>
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60 <inputs>
1
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61 <param format="fasta,fastq" name="input_reads" type="data" label="Querying sequences" help="In FASTA or FASTQ format (--reads)"/>
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62 <conditional name="sequencing_type">
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63 <param name="sequencing_type_selector" type="select" label="Sequencing type">
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64 <option value="not_paired">Reads are not paired</option>
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65 <option value="paired">Reads are paired</option>
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66 </param>
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67 <when value="paired">
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68 <param name="paired_type" type="select" display="radio" label="If one of the paired-end reads aligns and the other one does not">
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69 <option value="">leave the reads split between aligned and rejected files</option>
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70 <option value="--paired-in">output both reads to aligned file (--paired-in)</option>
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71 <option value="--paired-out">output both reads to rejected file (--paired-out)</option>
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72 </param>
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73 </when>
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74 </conditional>
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75
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76 <param name="strand_search" type="select" label="Which strands to search" display="radio">
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77 <option value="">Search both strands</option>
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78 <option value="-F">Search only the forward strand (-F)</option>
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79 <option value="-R">Search only the reverse-complementary strand (-R)</option>
0
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80 </param>
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81
1
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82 <conditional name="databases_type">
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83 <param name="databases_selector" type="select" label="Databases to query"
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84 help="Public rRNA databases provided with SortMeRNA have been indexed.
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85 On the contrary, personal databases must be indexed each time SortMeRNA is launched.
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86 Please be patient, this may take some time depending on the size of the given database.">
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87 <option value="cached" selected="true">Public ribosomal databases</option>
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88 <option value="history">Databases from your history</option>
0
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89 </param>
1
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90 <when value="cached">
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91 <param name="input_databases" label="rRNA database" type="select" display="checkboxes" multiple="true">
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92 <options from_data_table="rRNA_databases" />
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93 <validator type="no_options" message="Select at least one database"/>
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94 </param>
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95 </when>
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96 <when value="history">
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97 <repeat name="input_databases" title="Database" min="1">
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98 <param name="database_name" type="data" format="fasta" label="rRNA database"
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99 help="Your database will be indexed first, which may take up to several minutes."/>
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100 </repeat>
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101 </when>
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102 </conditional>
0
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103
1
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104 <!-- Outputs -->
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105 <conditional name="aligned_fastx">
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106 <param name="aligned_fastx_selector" type="select" label="Include aligned reads in FASTA/FASTQ format">
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107 <option value="--fastx">Yes (--fastx)</option>
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108 <option value="">No</option>
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109 </param>
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110 <when value="--fastx">
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111 <param name="other" type="boolean" label="Include rejected reads file" help="(--other)" />
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112 </when>
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113 <when value="" />
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114 </conditional>
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115 <conditional name="aligned_sam">
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116 <param name="aligned_sam_selector" type="select" label="Include alignments in SAM format">
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117 <option value="--sam">Yes (--sam)</option>
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118 <option value="">No</option>
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119 </param>
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120 <when value="--sam">
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121 <param name="sq" type="boolean" truevalue="--SQ" falsevalue="" label="Add SQ tags to the SAM file" help="(--SQ)" />
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122 </when>
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123 <when value="" />
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124 </conditional>
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125 <param name="aligned_blast" type="select" label="Include alignments in BLAST-like format">
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126 <option value="--blast 0">pairwise (--blast 0)</option>
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127 <option value="--blast 1">tabular BLAST -m 8 format (--blast 1)</option>
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128 <option value="--blast 2">tabular + column for CIGAR (--blast 2)</option>
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129 <option value="--blast 3">tabular + columns for CIGAR and query coverage (--blast 3)</option>
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130 <option value="" selected="true">No</option>
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131 </param>
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132 <param name="log" type="boolean" checked="False" truevalue="--log" falsevalue="" label="Generate statistics file"
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133 help="Generates statistics for the rRNA content of reads, as well as rRNA subunit distribution. (--log)">
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134 </param>
0
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135 </inputs>
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136 <outputs>
1
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137 <data format_source="input_reads" name="output_fastx" from_work_dir="aligned.dat"
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138 label="Aligned reads on ${on_string} (${input_reads.datatype.file_ext})">
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139 <filter>aligned_fastx.aligned_fastx_selector</filter>
0
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140 </data>
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141 <data format_source="input_reads" name="output_other" from_work_dir="other_file.dat"
1
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142 label="Rejected reads on ${on_string} (${input_reads.datatype.file_ext})">
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143 <filter>aligned_fastx.aligned_fastx_selector and aligned_fastx.other</filter>
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144 </data>
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145 <data format="sam" name="output_sam" from_work_dir="aligned.sam"
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146 label="Alignments on ${on_string} (SAM)">
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147 <filter>aligned_sam.aligned_sam_selector</filter>
0
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148 </data>
1
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149 <data format="tabular" name="output_blast" from_work_dir="aligned.blast"
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150 label="Alignments on ${on_string} (SAM)">
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151 <filter>aligned_blast</filter>
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152 <change_format>
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153 <when input="aligned_blast" value="--blast 0" format="txt" />
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154 </change_format>
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155 </data>
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156 <data format="txt" name="output_log" label="${tool.name} statistics (txt)" from_work_dir="aligned.log">
0
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157 <filter>log</filter>
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158 </data>
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159 </outputs>
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160 <tests>
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161 <test>
1
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162 <param name="input_reads" value="read_small.fastq" />
0
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163 <param name="sequencing_type_selector" value="not_paired" />
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164 <param name="strand_search" value="" />
1
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165 <param name="databases_selector" value="history" />
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166 <param name="database_name" value="ref_small.fasta" />
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167 <param name="other" value="True" />
0
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168 <param name="log" value="" />
1
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169 <output name="output_fastx" file="sortmerna_wrapper_accept1.fastq" />
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170 <output name="output_other" file="sortmerna_wrapper_other1.fastq" />
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171 <output name="output_sam" file="sortmerna_wrapper_sam1.sam" lines_diff="2" />
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172 </test>
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173 <test>
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174 <param name="input_reads" value="read_small.fasta" />
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175 <param name="sequencing_type_selector" value="not_paired" />
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176 <param name="strand_search" value="" />
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177 <param name="databases_selector" value="history" />
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178 <param name="database_name" value="ref_small.fasta" />
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179 <param name="other" value="True" />
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180 <param name="log" value="" />
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181 <output name="output_fastx" file="sortmerna_wrapper_accept2.fasta" />
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182 <output name="output_other" file="sortmerna_wrapper_other2.fasta" />
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183 <output name="output_sam" file="sortmerna_wrapper_sam2.sam" lines_diff="2" />
0
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184 </test>
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185 </tests>
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186 <help>
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187 <![CDATA[
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188 **What it does**
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189
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190 SortMeRNA_ is a software designed to rapidly filter ribosomal RNA fragments
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191 from metatransriptomic data produced by next-generation sequencers.
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192 It is capable of handling large RNA databases and sorting out all fragments
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193 matching to the database with high accuracy and specificity.
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194
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195 .. _SortMeRNA: http://bioinfo.lifl.fr/RNA/sortmerna/
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196
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197
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198 **Input**
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199
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200 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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201 If the user has two foward-reverse paired-sequencing reads files, they may use
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202 the script "merge_paired_reads.sh" to interleave the reads into one file, preserving their order.
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203
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204 If the sequencing type for the reads is paired-ended, the user has two options under
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205 "Sequencing type" to filter the reads and preserve their order in the file.
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206 For a further example of each option, please refer to Section 4.2.3 in the `SortMeRNA User Manual`_.
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207
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208 .. _sortmerna user manual: http://bioinfo.lifl.fr/RNA/sortmerna/code/SortMeRNA-user-manual-v1.7.pdf
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209
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210
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211 **Output**
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212
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213 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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214
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215
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216 **rRNA databases**
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217
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218 SortMeRNA is distributed with 8 representative rRNA databases, which were
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219 all constructed from the SILVA SSU,LSU (version 111) and the RFAM 5/5.8S
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220 (version 11.0) databases using the tool UCLUST.
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221
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222 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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223 | Representative database | id % | average id% | # seq (clustered) | Origin | # seq (original) |
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224 +==========================+======+=============+===================+========================+===================+
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225 | SILVA 16S bacteria | 85 | 91.6 | 8174 | SILVA SSU Ref NR v.111 | 244077 |
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226 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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227 | SILVA 16S archaea | 95 | 96.7 | 3845 | SILVA SSU Ref NR v.111 | 10919 |
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228 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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229 | SILVA 18S eukarya | 95 | 96.7 | 4512 | SILVA SSU Ref NR v.111 | 31862 |
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230 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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231 | SILVA 23S bacteria | 98 | 99.4 | 3055 | SILVA LSU Ref v.111 | 19580 |
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232 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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233 | SILVA 23s archaea | 98 | 99.5 | 164 | SILVA LSU Ref v.111 | 405 |
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234 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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235 | SILVA 28S eukarya | 98 | 99.1 | 4578 | SILVA LSU Ref v.111 | 9321 |
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236 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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237 | Rfam 5S archaea/bacteria | 98 | 99.2 | 59513 | RFAM | 116760 |
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238 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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239 | Rfam 5.8S eukarya | 98 | 98.9 | 13034 | RFAM | 225185 |
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240 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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241
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242 id %: members of the cluster must have identity at least 'id %' identity with the representative sequence
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244 average id %: average identity of a cluster member to the representative sequence
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246 The user may also choose to use their own rRNA databases.
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247
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248 .. class:: warningmark
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249
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250 Note that your personal databases are indexed each time, and that
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251 this may take some time depending on the size of the given database.
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252 ]]>
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253 </help>
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254
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255 <citations>
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256 <citation type="doi">10.1093/bioinformatics/bts611</citation>
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257 <citation type="doi">10.1093/nar/gks1219</citation>
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258 <citation type="doi">10.1093/nar/gks1005</citation>
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259 <citation type="doi">10.1093/bioinformatics/btq461</citation>
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260 <citation type="doi">10.1038/nbt.2198</citation>
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261 </citations>
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262 </tool>