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annotate sortmerna.xml @ 6:185effcdfb68 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf
author rnateam
date Tue, 06 Jun 2017 13:41:03 -0400
parents cd8c76234b0c
children 1eafcc450052
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185effcdfb68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf
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1 <tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@VERSION@.4">
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2 <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description>
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3 <macros>
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4 <import>macros.xml</import>
cd8c76234b0c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@VERSION@">sortmerna</requirement>
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8 </requirements>
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9 <stdio>
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10 <regex match="This program builds a Burst trie on an input rRNA database"
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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11 source="both"
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12 level="fatal"
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13 description="Buildtrie program failed to execute." />
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14 <regex match="The database name"
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15 source="both"
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16 level="fatal"
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17 description="The database ${databases} has not been preprocessed using buildtrie before using SortMeRNA." />
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18 <regex match="ERROR"
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19 source="both"
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20 level="fatal"
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21 description="ERROR" />
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22 </stdio>
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23 <version_command>
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24 <![CDATA[
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25 sortmerna --version 2>&1|grep 'SortMeRNA version'
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26 ]]>
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27 </version_command>
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28 <command>
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29 <![CDATA[
1
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30 #set $ref = ''
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31 #set $sep=''
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32 #if str( $databases_type.databases_selector ) == 'history'
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33 #for $db in $databases_type.database_name
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34 #set $ref += $sep + str($db) + ',' + $os.path.splitext($os.path.basename(str($db)))[0]
b482293b2987 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 844d980a7de5f199487ca9591420a23df63c5246-dirty
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35 #set $sep = ':'
b482293b2987 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 844d980a7de5f199487ca9591420a23df63c5246-dirty
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36 #end for
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37 #else if str( $databases_type.databases_selector ) == 'cached_to_index'
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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38 ## databases path is not directly accessible, must match by hand with LOC file contents
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185effcdfb68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf
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39 #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data])
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40 #for $db in $databases_type.input_databases.value
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41 #set $ref += $sep + $data_table[$db] + '.fasta,' + $data_table[$db] + '-reindexed'
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42 #set $sep = ':'
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43 #end for
1
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44 #else:
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45 ## databases path is not directly accessible, must match by hand with LOC file contents
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46 #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data])
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47 #for $db in $databases_type.input_databases.value
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48 #set $ref += $sep + $data_table[$db] + '.fasta,' + $data_table[$db]
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49 #set $sep = ':'
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50 #end for
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51 #end if
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52
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53 #if str( $databases_type.databases_selector ) != 'cached':
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54 indexdb_rna
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55 --ref $ref
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56 -L $databases_type.seed_length
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57 --max_pos $databases_type.max_pos
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58 &&
1
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59 #end if
2
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60
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61 sortmerna
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62 --ref $ref
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63 --reads $input_reads
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64 --aligned aligned
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65
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66 #if str( $sequencing_type.sequencing_type_selector ) == 'paired'
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67 $sequencing_type.paired_type
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68 #end if
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69
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70 $strand_search
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71 $aligned_fastx.aligned_fastx_selector
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72 #if $aligned_fastx.aligned_fastx_selector == '--fastx'
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73 #if $aligned_fastx.other
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74 --other other_file
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75 #end if
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76 #end if
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77 $aligned_sam.aligned_sam_selector
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78 #if $aligned_sam.aligned_sam_selector == '--sam'
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79 $aligned_sam.sq
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80 #end if
3
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81 #if $aligned_blast.aligned_blast_selector == '--blast'
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82 --blast "$aligned_blast.aligned_blast_format"
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83 #end if
2
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84
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85 $log
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86
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87 #if $report.report_type == 'best'
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88 #if $report.report_best.report_best_type == '1'
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89 --best 1
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90 --min_lis $report.report_best.report_best_min_lis
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91 #else
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92 --best $report.report_best.report_best_value
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93 --min_lis $report.report_best.report_best_min_lis
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94 #end if
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95 #else
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96 #if $report.report_num_alignments.report_num_alignments_type == 'other_value'
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97 --num_alignments $report.report_num_alignments.report_num_alignments_value
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98 #else
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99 --num_alignments $report.report_num_alignments.report_num_alignments_type
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100 #end if
0
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101 #end if
2
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102
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103 -e $e_value
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104 --match $match
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105 --mismatch $mismatch
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106 --gap_open $gap_open
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107 --gap_ext $gap_ext
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108 -N $ambiguous_letter
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109 -a \${GALAXY_SLOTS:-1}
0
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110 ]]>
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111 </command>
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112 <inputs>
1
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113 <param format="fasta,fastq" name="input_reads" type="data" label="Querying sequences" help="In FASTA or FASTQ format (--reads)"/>
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114 <conditional name="sequencing_type">
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115 <param name="sequencing_type_selector" type="select" label="Sequencing type">
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116 <option value="not_paired">Reads are not paired</option>
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117 <option value="paired">Reads are paired</option>
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118 </param>
2
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119 <when value="not_paired" />
1
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120 <when value="paired">
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121 <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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122 <option value="">leave the reads split between aligned and rejected files</option>
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123 <option value="--paired_in">output both reads to aligned file (--paired_in)</option>
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124 <option value="--paired_out">output both reads to rejected file (--paired_out)</option>
1
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125 </param>
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126 </when>
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127 </conditional>
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128
2
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129 <param name="strand_search" type="select" label="Which strands to search">
1
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130 <option value="">Search both strands</option>
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131 <option value="-F">Search only the forward strand (-F)</option>
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132 <option value="-R">Search only the reverse-complementary strand (-R)</option>
0
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133 </param>
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134
1
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135 <conditional name="databases_type">
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136 <param name="databases_selector" type="select" label="Databases to query"
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137 help="Public rRNA databases provided with SortMeRNA have been indexed.
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138 On the contrary, personal databases must be indexed each time SortMeRNA is launched.
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139 Please be patient, this may take some time depending on the size of the given database.">
2
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140 <option value="cached" selected="true">Public pre-indexed ribosomal databases</option>
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141 <option value="cached_to_index">Public ribosomal databases to index with non default parameters</option>
1
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142 <option value="history">Databases from your history</option>
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143 </param>
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144 <when value="cached">
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145 <param name="input_databases" label="rRNA databases" type="select" display="checkboxes" multiple="true">
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146 <options from_data_table="rRNA_databases" />
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147 <validator type="no_options" message="Select at least one database"/>
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148 </param>
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149 </when>
2
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150 <when value="cached_to_index">
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151 <param name="input_databases" label="rRNA databases" type="select" display="checkboxes" multiple="true">
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152 <options from_data_table="rRNA_databases" />
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153 <validator type="no_options" message="Select at least one database"/>
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154 </param>
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155 <param name="seed_length" type="integer" min="0" max="100" value="18" label="Seed length for database indexing" help="(-L)"/>
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156 <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 (--max_pos)"/>
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157 </when>
1
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158 <when value="history">
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159 <param name="database_name" type="data" format="fasta" multiple="true" label="rRNA databases"
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160 help="Your databases will be indexed first, which may take up to several minutes."/>
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161 <param name="seed_length" type="integer" min="0" max="100" value="18" label="Seed length for database indexing" help="(-L)"/>
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162 <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 (--max_pos)"/>
1
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163 </when>
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164 </conditional>
0
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165
1
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166 <!-- Outputs -->
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167 <conditional name="aligned_fastx">
2
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168 <param name="aligned_fastx_selector" type="select" label="Include aligned reads in FASTA/FASTQ format?">
1
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169 <option value="--fastx">Yes (--fastx)</option>
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170 <option value="">No</option>
0
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171 </param>
1
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172 <when value="--fastx">
2
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173 <param name="other" type="boolean" label="Include rejected reads file?" help="(--other)" />
1
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174 </when>
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175 <when value="" />
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176 </conditional>
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177 <conditional name="aligned_sam">
2
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178 <param name="aligned_sam_selector" type="select" label="Include alignments in SAM format?">
1
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179 <option value="--sam">Yes (--sam)</option>
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180 <option value="">No</option>
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181 </param>
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182 <when value="--sam">
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183 <param name="sq" type="boolean" truevalue="--SQ" falsevalue="" label="Add SQ tags to the SAM file" help="(--SQ)" />
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184 </when>
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185 <when value="" />
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186 </conditional>
3
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187 <conditional name="aligned_blast">
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188 <param name="aligned_blast_selector" type="select" label="Include alignments in BLAST-like format?">
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189 <option value="--blast">Yes</option>
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190 <option value="" selected="true">No</option>
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191 </param>
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192 <when value="--blast">
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193 <param name="aligned_blast_format" type="select" label="BLAST-like format?">
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194 <option value="0">pairwise (--blast '0')</option>
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195 <option value="1">tabular BLAST -m 8 format (--blast '1')</option>
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196 <option value="1 cigar">tabular + column for CIGAR (--blast '1 cigar')</option>
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197 <option value="1 cigar qcov">tabular + columns for CIGAR and query coverage (--blast '1 cigar qcov')</option>
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198 <option value="1 cigar qcov qstrand">tabular + columns for CIGAR, query coverage and strand (--blast '1 cigar qcov qstrand')</option>
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199 </param>
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200 </when>
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201 <when value="" />
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202 </conditional>
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203 <param name="log" type="boolean" checked="false" truevalue="--log" falsevalue="" label="Generate statistics file"
1
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204 help="Generates statistics for the rRNA content of reads, as well as rRNA subunit distribution. (--log)">
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205 </param>
2
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206 <conditional name="report">
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207 <param name="report_type" type="select" label="Parameters for filtering and read mapping" help="">
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208 <option value="best" selected="true">Report best alignments per read reaching E-value</option>
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209 <option value="num_alignments">Report first alignements per read reaching E-value</option>
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210 </param>
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211 <when value="best">
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212 <conditional name="report_best">
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213 <param name="report_best_type" type="select" label="Number of searched alignments" help="Only the best alignment is reported (--best)">
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214 <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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215 <option value="other_value">A custom number of reference sequences are searched for alignments (speed decrease for high value)</option>
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216 </param>
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217 <when value="1">
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218 <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. (--min_lis)"/>
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219 </when>
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220 <when value="other_value">
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221 <param name="report_best_value" type="integer" min="2" max="100" value="2" 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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222 <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. (--min_lis)"/>
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223 </when>
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224 </conditional>
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225 </when>
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226 <when value="num_alignments">
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227 <conditional name="report_num_alignments">
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228 <param name="report_num_alignments_type" type="select" label="Number of output alignments" help="(--num_alignments)">
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229 <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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230 <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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231 <option value="other_value">A custom number of alignments are made and reported (speed decrease for high value)</option>
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232 </param>
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233 <when value="0" />
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234 <when value="1" />
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235 <when value="other_value">
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236 <param name="report_num_alignments_value" type="integer" min="0" max="100" value="1" label="Number of alignments to be made and reported" help=""/>
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237 </when>
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238 </conditional>
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239 </when>
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240 </conditional>
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241
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242 <param name="e_value" type="float" min="0" max="10" value="1" label="E-value threshold" help="(-e)"/>
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243 <param name="match" type="integer" min="0" max="10" value="2" label="SW score for a match" help="(--match)"/>
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244 <param name="mismatch" type="integer" min="-10" max="0" value="-3" label="SW penalty for a mismatch" help="(--mismatch)"/>
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245 <param name="gap_open" type="integer" min="0" max="10" value="5" label="SW penalty for introducing a gap" help="(--gap_open)"/>
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246 <param name="gap_ext" type="integer" min="0" max="10" value="2" label="SW penalty for extending a gap" help="(--gap_ext)"/>
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247 <param name="ambiguous_letter" type="integer" min="-10" max="0" value="-3" label="SW penalty for ambiguous letters (N's)" help="(-N)"/>
0
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248 </inputs>
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249 <outputs>
1
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250 <data format_source="input_reads" name="output_fastx" from_work_dir="aligned.dat"
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251 label="Aligned reads on ${on_string} (${input_reads.datatype.file_ext})">
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252 <filter>aligned_fastx['aligned_fastx_selector']</filter>
0
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253 </data>
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254 <data format_source="input_reads" name="output_other" from_work_dir="other_file.dat"
1
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255 label="Rejected reads on ${on_string} (${input_reads.datatype.file_ext})">
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256 <filter>aligned_fastx['aligned_fastx_selector'] and aligned_fastx['other']</filter>
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257 </data>
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258 <data format="sam" name="output_sam" from_work_dir="aligned.sam"
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259 label="Alignments on ${on_string} (SAM)">
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260 <filter>aligned_sam['aligned_sam_selector']</filter>
0
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261 </data>
1
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262 <data format="tabular" name="output_blast" from_work_dir="aligned.blast"
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263 label="Alignments on ${on_string} (BLAST)">
3
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264 <filter>aligned_blast['aligned_blast_selector']</filter>
1
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265 <change_format>
3
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266 <when input="aligned_blast.aligned_blast_format" value="0" format="txt" />
1
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267 </change_format>
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268 </data>
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269 <data format="txt" name="output_log" label="${tool.name} statistics (txt)" from_work_dir="aligned.log">
0
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270 <filter>log</filter>
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271 </data>
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272 </outputs>
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273 <tests>
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274 <test>
1
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275 <param name="input_reads" value="read_small.fastq" />
0
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276 <param name="sequencing_type_selector" value="not_paired" />
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277 <param name="strand_search" value="" />
1
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278 <param name="databases_selector" value="history" />
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279 <param name="database_name" value="ref_small.fasta" />
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280 <param name="aligned_fastx_selector" value="--fastx" />
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281 <param name="other" value="True" />
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282 <param name="aligned_sam_selector" value="--sam" />
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283 <param name="aligned_blast_selector" value="--blast"/>
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284 <param name="aligned_blast_format" value="1 cigar qcov" />
0
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285 <param name="log" value="" />
3
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286 <param name="report_type" value="best" />
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287 <param name="report_best_type" value="1" />
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288 <param name="e_value" value="1"/>
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289 <param name="match" value="2"/>
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290 <param name="mismatch" value="-3" />
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291 <param name="gap_open" value="5"/>
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292 <param name="gap_ext" value="2"/>
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293 <param name="ambiguous_letter" value="-3"/>
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294 <output name="output_fastx" file="sortmerna_wrapper_accept1.fastq" />
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295 <output name="output_other" file="sortmerna_wrapper_other1.fastq" />
1
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296 <output name="output_sam" file="sortmerna_wrapper_sam1.sam" lines_diff="2" />
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297 </test>
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298 <test>
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299 <param name="input_reads" value="read_small.fasta" />
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300 <param name="sequencing_type_selector" value="not_paired" />
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301 <param name="strand_search" value="" />
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302 <param name="databases_selector" value="history" />
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303 <param name="database_name" value="ref_small.fasta" />
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304 <param name="aligned_fastx_selector" value="--fastx" />
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305 <param name="other" value="True" />
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306 <param name="aligned_sam_selector" value="--sam" />
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307 <param name="aligned_blast" value="" />
1
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308 <param name="log" value="" />
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309 <param name="report_type" value="best" />
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310 <param name="report_best_type" value="1" />
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311 <param name="report_type" value="best" />
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312 <param name="report_best_type" value="1" />
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313 <param name="e_value" value="1"/>
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314 <param name="match" value="2"/>
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315 <param name="mismatch" value="-3" />
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316 <param name="gap_open" value="5"/>
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317 <param name="gap_ext" value="2"/>
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318 <param name="ambiguous_letter" value="-3"/>
1
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319 <output name="output_fastx" file="sortmerna_wrapper_accept2.fasta" />
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320 <output name="output_other" file="sortmerna_wrapper_other2.fasta" />
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321 <output name="output_sam" file="sortmerna_wrapper_sam2.sam" lines_diff="2" />
0
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322 </test>
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323 </tests>
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324 <help>
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325 <![CDATA[
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326 **What it does**
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327
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328 SortMeRNA_ is a software designed to rapidly filter ribosomal RNA fragments
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329 from metatransriptomic data produced by next-generation sequencers.
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330 It is capable of handling large RNA databases and sorting out all fragments
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331 matching to the database with high accuracy and specificity.
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332
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333 .. _SortMeRNA: http://bioinfo.lifl.fr/RNA/sortmerna/
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334
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335
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336 **Input**
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337
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338 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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339 If the user has two foward-reverse paired-sequencing reads files, they may use
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340 the script "merge_paired_reads.sh" to interleave the reads into one file, preserving their order.
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341
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342 If the sequencing type for the reads is paired-ended, the user has two options under
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343 "Sequencing type" to filter the reads and preserve their order in the file.
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344 For a further example of each option, please refer to Section 4.2.3 in the `SortMeRNA User Manual`_.
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345
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346 .. _sortmerna user manual: http://bioinfo.lifl.fr/RNA/sortmerna/code/SortMeRNA-user-manual-v1.7.pdf
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347
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348
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349 **Output**
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350
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351 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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352
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353
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354 **rRNA databases**
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355
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356 SortMeRNA is distributed with 8 representative rRNA databases, which were
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357 all constructed from the SILVA SSU,LSU (version 111) and the RFAM 5/5.8S
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358 (version 11.0) databases using the tool UCLUST.
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359
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360 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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361 | Representative database | id % | average id% | # seq (clustered) | Origin | # seq (original) |
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362 +==========================+======+=============+===================+========================+===================+
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363 | SILVA 16S bacteria | 85 | 91.6 | 8174 | SILVA SSU Ref NR v.111 | 244077 |
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364 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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365 | SILVA 16S archaea | 95 | 96.7 | 3845 | SILVA SSU Ref NR v.111 | 10919 |
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366 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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367 | SILVA 18S eukarya | 95 | 96.7 | 4512 | SILVA SSU Ref NR v.111 | 31862 |
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368 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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369 | SILVA 23S bacteria | 98 | 99.4 | 3055 | SILVA LSU Ref v.111 | 19580 |
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370 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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371 | SILVA 23s archaea | 98 | 99.5 | 164 | SILVA LSU Ref v.111 | 405 |
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372 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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373 | SILVA 28S eukarya | 98 | 99.1 | 4578 | SILVA LSU Ref v.111 | 9321 |
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374 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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375 | Rfam 5S archaea/bacteria | 98 | 99.2 | 59513 | RFAM | 116760 |
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376 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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377 | Rfam 5.8S eukarya | 98 | 98.9 | 13034 | RFAM | 225185 |
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378 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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379
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380 id %: members of the cluster must have identity at least 'id %' identity with the representative sequence
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381
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382 average id %: average identity of a cluster member to the representative sequence
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383
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384 The user may also choose to use their own rRNA databases.
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385
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386 .. class:: warningmark
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387
2
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388 Note that your personal databases are indexed each time. The public ribosomal
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389 databases are indexed when added, but they can be re-indexed with non-default indexing
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390 parameters. The indexing may take some time depending on the size of the given database.
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391
0
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392 ]]>
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393 </help>
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394
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395 <citations>
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396 <citation type="doi">10.1093/bioinformatics/bts611</citation>
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397 <citation type="doi">10.1093/nar/gks1219</citation>
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398 <citation type="doi">10.1093/nar/gks1005</citation>
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399 <citation type="doi">10.1093/bioinformatics/btq461</citation>
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400 <citation type="doi">10.1038/nbt.2198</citation>
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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401 </citations>
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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402 </tool>