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annotate split_libraries.xml @ 0:c1bd0c560018 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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0
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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1 <tool id="qiime_split_libraries" name="Split libraries" version="1.9.1">
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2 <description>according to barcodes specified in mapping file</description>
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3
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7
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8 <expand macro="requirements" />
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9
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10 <version_command><![CDATA[
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11 split_libraries.py --version
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12 ]]></version_command>
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13
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14 <command><![CDATA[
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15 split_libraries.py
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16 -m $mapping_fp
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17 -o split_libraries
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18
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19 #set $seq_files = ''
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20 #set $sep = ''
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21 #for $file in $input_files_fasta
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22 #set $seq_files += $sep + str($file)
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23 #set $sep = ','
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24 #end for
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25 -f $seq_files
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26
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27 #if str($input_files_qual) != 'None':
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28 set $files = ''
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29 #set $sep = ''
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30 #for $file in $input_files_qual
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31 #set $files += $sep + str($file)
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32 #set $sep = ','
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33 #end for
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34 -q $files
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35 #end if
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36
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37 -l $min_seq_length
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38 -L $max_seq_length
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39 $trim_seq_length
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40
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41 $keep_primer
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42 $keep_barcode
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43
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44 -a $max_ambig
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45 -H $max_homopolymer
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46 -M $max_primer_mismatch
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47
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48 #if str( $barcode_type.barcode_selector ) != "custom_length"
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49 -b $barcode_type.barcode_selector
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50 #else
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51 -b $barcode_type.barcode_length
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52 #end if
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53
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54 -e $max_barcode_errors
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55 -n $start_numbering_at
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56 $retain_unassigned_reads
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57 $disable_bc_correction
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58
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59 #if str($input_files_qual) != 'None':
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60 -s $min_qual_score
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61 -w $qual_score_window
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62 $discard_bad_windows
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63 $record_qual_scores
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64 #end if
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65
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66 $disable_primers
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67
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68 $reverse_primers.reverse_primers_test
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69 #if str($reverse_primers.reverse_primers_test) == '--reverse_primers':
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70 --reverse_primer_mismatches $reverse_primers.reverse_primer_mismatches
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71 #end if
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72
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73 #if str($median_length_filtering):
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74 -i $median_length_filtering
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75 #end if
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76
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77 #if str($added_demultiplex_field):
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78 -j $added_demultiplex_field
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79 #end if
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80 ]]>
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81 </command>
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82
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83 <inputs>
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84 <param name="mapping_fp" label="Metadata mapping filepath" type="data"
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85 format="tabular,txt,tsv,csv" help="The file must contain header
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86 line indicating SampleID in the first column and BarcodeSequence in
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87 the second, LinkerPrimerSequence in the third. It is recommended to
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88 check the mapping file using the dedicated file (-m/--mapping_fp)"/>
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89
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90 <param name="input_files_fasta" type="data" format="fasta"
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91 label="Input fasta files" multiple="True" help="(-f/--fasta)"/>
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92
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93 <param name="input_files_qual" type="data"
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94 format="qual,qual454,qualillumina,qualsolexa,qualsolid"
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95 label="Input quality files (optional)" multiple="True"
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96 help="(-q/--qual)" optional="True"/>
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97
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98 <param name="min_seq_length" type="integer" value="200"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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99 label="Minimum sequence length" help="(-l/--min_seq_length)"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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diff changeset
100
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101 <param name="max_seq_length" type="integer" value="1000"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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102 label="Maximum sequence length" help="(-L/--max_seq_length)"/>
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103
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104 <param name="trim_seq_length" type="boolean" label="Compute sequence
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105 lengths after trimming and barcodes?" truevalue="-t" falsevalue=""
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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106 selected="False" help="(-t/--trim_seq_length)" />
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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diff changeset
107
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108 <param name="min_qual_score" type="integer" value="25"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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109 label="Minimum average quality score allowed in read"
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110 help="(-s/--min_qual_score)"/>
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111
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112 <param name="keep_primer" type="boolean" label="Remove primer from
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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113 sequences?" truevalue="" falsevalue="--keep_primer"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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114 selected="True" help="(-k/--keep_primer)" />
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115
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116 <param name="keep_barcode" type="boolean" label="Remove barcode from
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117 sequences?" truevalue="" falsevalue="--keep_barcode"
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118 selected="True" help="(-B/--keep_barcode)" />
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119
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120 <param name="max_ambig" type="integer" value="6"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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121 label="Maximum number of ambiguous bases" help="(-a/--max_ambig)"/>
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122
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123 <param name="max_homopolymer" type="integer" value="6"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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124 label="Maximum length of homopolymer run" help="(-H/--max_homopolymer)"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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125
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126 <param name="max_primer_mismatch" type="integer" value="0"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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127 label="Maximum number of primer mismatch" help="(-M/--max_primer_mismatch)"/>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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128
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129 <conditional name="barcode_type">
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130 <param name="barcode_selector" type="select" label="Type of barcode"
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131 help="(-b/ --barcode_type)">
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132 <option value="hamming_8">hamming_8</option>
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133 <option value="golay_12" selected="true">golay_12</option>
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134 <option value="variable_length">variable_length (disable any barcode correction)</option>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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135 <option value="custom_length">Custom length</option>
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diff changeset
136 </param>
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diff changeset
137 <when value="hamming_8" />
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diff changeset
138 <when value="golay_12" />
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diff changeset
139 <when value="variable_length" />
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140 <when value="custom_length">
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141 <param name="barcode_length" type="integer" value="4"
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142 label="Barcode length"/>
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143 </when>
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144 </conditional>
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145
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146 <param name="max_barcode_errors" type="float" value="1.5"
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147 label="Maximum number of errors in barcode"
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148 help="(-e/--max_barcode_errors)"/>
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149
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150 <param name="start_numbering_at" type="integer" value="1"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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151 label="Sequence id to use for the first seuqence"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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152 help="(-n/--start_numbering_at)"/>
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153
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154 <param name="retain_unassigned_reads" type="boolean" label="Retain
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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155 sequences with are Unassigned in the output sequence file?"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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156 truevalue="--retain_unassigned_reads" falsevalue=""
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157 selected="False" help="(--retain_unassigned_reads)" />
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158
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159 <param name="retain_unassigned_reads" type="boolean" label="Retain
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diff changeset
160 sequences with are Unassigned in the output sequence file?"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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161 truevalue="--retain_unassigned_reads" falsevalue=""
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162 selected="False" help="(--retain_unassigned_reads)" />
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163
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164 <param name="disable_bc_correction" type="boolean" label="Disable attempts
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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165 to find nearest corrected barcode?"
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166 truevalue="(--disable_bc_correction)" falsevalue=""
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167 selected="False" help="It can improve performance.
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168 (-c/--disable_bc_correction)" />
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169
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170 <param name="qual_score_window" type="integer" value="0"
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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171 label="Size of the sliding window" help="If the average score of a
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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172 continuous set of w nucleotides falls below the threshold, the sequence
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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173 is discarded. A good value would be 50. 0 (zero) means no filtering.
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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174 Must pass a .qual file (see -q parameter) if this functionality is
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175 enabled. Default behavior for this function is to truncate the sequence
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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176 at the beginning of the poor quality window, and test for minimal
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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177 length (-l parameter) of the resulting sequence (-w/--qual_score_window)"/>
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178
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179 <param name="discard_bad_windows" type="boolean" label="Discard any
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180 sequences where a bad window is found?"
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181 truevalue="--discard_bad_windows" falsevalue=""
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182 selected="False" help="It will work if the sliding window length is bigger
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183 than 0 (-g/--discard_bad_windows)" />
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184
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185 <param name="disable_primers" type="boolean" label="Disable primer usage
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186 when demultiplexing?" truevalue="--disable_primers" falsevalue=""
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187 selected="False" help="It should be enabled for unusual circumstances,
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188 such as analyzing Sanger sequence data generated with different primers
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189 (-p/--disable_primers)" />
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190
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191 <conditional name="reverse_primers">
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192 <param name="reverse_primers_test" type="select" label="Enable removal
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193 of the reverse primer and any subsequence sequence from the end
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194 of each read?" help="(-z/--reverse_primers)" >
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195 <option value="--reverse_primers">Yes</option>
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196 <option value="" selected="true">No</option>
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197 </param>
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198 <when value="" />
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199 <when value="--reverse_primers" >
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200 <param name="reverse_primer_mismatches" type="integer" value="0"
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201 label="Number of allowed mismatches for reverse primers"
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202 help="(--reverse_primer_mismatches)"/>
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203 </when>
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204 </conditional>
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205
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206 <param name="record_qual_scores" type="boolean" label="Record quality
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207 scores for all sequences that are recorded?" truevalue="--record_qual_scores"
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208 falsevalue="" selected="False" help="If this option is enabled, a file
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209 named seqs_filtered.qual will be created in the output directory, and
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210 will contain the same sequence IDs in the seqs.fna file and sequence
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211 quality scores matching the bases present in the seqs.fna file
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212 (-d/--record_qual_scores)" />
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213
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214 <param name="median_length_filtering" type="integer"
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215 label="Median length filtering (optional)" help="It disables minimum
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216 and maximum sequence length filtering, and instead calculates the median
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217 sequence length and filters the sequences based upon the number of median
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218 absolute deviations specified by this parameter. Any sequences with
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219 lengths outside the number of deviations will be removed
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220 (-i/--median_length_filtering)"
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221 optional="True"/>
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222
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223 <param name="added_demultiplex_field" type="text" label="Field
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224 to use in the mapping file as additional demultiplexing (optional)"
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225 help="It can be used with or without barcodes. All combinations of
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226 barcodes/primers and these fields must be unique. The fields must contain
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227 values that can be parsed from the fasta labels such as 'plate=R_2008_12_09'.
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228 In this case, 'plate' would be the column header and 'R_2008_12_09'
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229 would be the field data (minus quotes) in the mapping file.
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230 To use the run prefix from the fasta label, such as 'FLP3FBN01ELBSX',
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231 where 'FLP3FBN01' is generated from the run ID, use 'run_prefix' and
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232 set the run prefix to be used as the data under the column header
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233 'run_prefix' (-j/--added_demultiplex_field)" optional="True"/>
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234
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235 <param name="truncate_ambi_bases" type="boolean" label="Enable to truncate
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236 at the first N character encountered in the sequences?"
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237 truevalue="--truncate_ambi_bases" falsevalue="" selected="False"
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238 help="This will disable testing for ambiguous bases
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239 (-x/--truncate_ambi_bases)"/>
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240 </inputs>
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241
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242 <outputs>
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243 <data name="sequences" format="fasta"
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244 from_work_dir="split_libraries/*.fna"
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245 label="${tool.name} on ${on_string}: sequences"/>
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246
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247 <data name="log" format="txt"
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248 from_work_dir="split_libraries/split_library_log.txt"
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249 label="${tool.name} on ${on_string}: log"/>
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250
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251 <data name="histograms" format="txt"
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252 from_work_dir="split_libraries/histograms.txt"
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253 label="${tool.name} on ${on_string}: histograms"/>
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254
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255 <data name="quality" format="qual,qual454,qualillumina,qualsolexa,qualsolid"
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256 from_work_dir="split_libraries/*.qual"
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257 label="${tool.name} on ${on_string}: quality">
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258 <filter>record_qual_scores is True</filter>
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259 </data>
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260 </outputs>
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261
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262 <tests>
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263 <test>
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264 </test>
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265 </tests>
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266
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267 <help><![CDATA[
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268
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269 **What it does**
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270
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271 This tool splits libraries according to barcodes specified in mapping file.
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272
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273 Since newer sequencing technologies provide many reads per run (e.g. the 454 GS FLX Titanium series can produce 400-600 million base pairs with 400-500 base pair read lengths) researchers are now finding it useful to combine multiple samples into a single 454 run. This multiplexing is achieved through the application of a pyrosequencing-tailored nucleotide barcode design (described in (Parameswaran et al., 2007)). By assigning individual, unique sample specific barcodes, multiple sequencing runs may be performed in parallel and the resulting reads can later be binned according to sample. The script %prog performs this task, in addition to several quality filtering steps including user defined cut-offs for: sequence lengths; end-trimming; minimum quality score. To summarize, by using the fasta, mapping, and quality files, the program %prog will parse sequences that meet user defined quality thresholds and then rename each read with the appropriate Sample ID, thus formatting the sequence data for downstream analysis. If a combination of different sequencing technologies are used in any particular study, %prog can be used to perform the quality-filtering for each library individually and the output may then be combined.
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274
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275 Sequences from samples that are not found in the mapping file (no corresponding barcode) and sequences without the correct primer sequence will be excluded. Additional scripts can be used to exclude sequences that match a given reference sequence (e.g. the human genome; exclude_seqs_by_blast.py) and/or sequences that are flagged as chimeras (identify_chimeric_seqs.py).
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276
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277 More information about this tool is available on
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278 `QIIME documentation <http://qiime.org/scripts/split_libraries.html>`_.
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279 ]]>
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280 </help>
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281
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282 <citations>
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283 <expand macro="citations" />
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284 </citations>
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285 </tool>