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annotate split_libraries_fastq.xml @ 0:c1bd0c560018 draft default tip

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author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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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="split_libraries_fastq" name="Split fastq libraries" version="1.9.1">
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2 <description>to performs demultiplexing of Fastq sequence data</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_fastq.py --version
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12 ]]>
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13 </version_command>
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15 <command><![CDATA[
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16 split_libraries_fastq.py
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17
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18 #set $seq_files = ''
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19 #set $sep = ''
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20 #for $file in $input_fastq_files
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21 #set $seq_files += $sep + str($file)
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22 #set $sep = ','
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23 #end for
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24 -i $seq_files
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25
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26 -o split_libraries
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27
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28 #set $mapping_files = ''
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29 #set $sep = ''
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30 #for $file in $input_mapping_files
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31 #set $mapping_files += $sep + str($file)
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32 #set $sep = ','
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33 #end for
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34 -m $mapping_files
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35
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36 #set $barcode_files = ''
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37 #set $sep = ''
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38 #for $file in $input_files_barcode_read_fps
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39 #set $barcode_files += $sep + str($file)
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40 #set $sep = ','
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41 #end for
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42 -b $barcode_files
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43
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44 $store_qual_scores
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45
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46 #if str($sample_ids):
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47 --sample_ids $sample_ids
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48 #end if
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49
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50 $store_demultiplexed_fastq
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51 $retain_unassigned_reads
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52 -r $max_bad_run_length
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53 -p $min_per_read_length_fraction
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54 -n $sequence_max_n
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55 -s $start_seq_id
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56
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57 $rev_comp_barcode
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58 $rev_comp_mapping_barcodes
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59 $rev_comp
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60
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61 -q $phred_quality_threshold
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62
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63 #if str( $barcode_type.barcode_selector ) != "custom_length"
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64 --barcode_type $barcode_type.barcode_selector
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65 #else
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66 --barcode_type $barcode_type.barcode_length
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67 #end if
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68
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69 --max_barcode_errors $max_barcode_errors
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70
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71 $phred_offset
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72 ]]>
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73 </command>
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74
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75 <inputs>
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76 <param name="input_fastq_files" type="data"
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77 format="fastq,fastqsanger,fastqsolexa"
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78 label="Input fastq files" multiple="True" help="(-i/--sequence_read_fps)"/>
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79
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80 <param name="input_mapping_files" type="data"
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81 format="txt,tabular,tsv,csv" label="Metadata mapping files (optional)"
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82 multiple="True" optional="True" help="(-m/--mapping_fps)"/>
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83
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84 <param name="input_files_barcode_read_fps" type="data"
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85 format="fastq,fastqsanger,fastqsolexa" label="Barcode read files (optional)"
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86 multiple="True" optional="True" help="(-b/--barcode_read_fps)"/>
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87
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88 <param name="store_qual_scores" type="boolean" label="Store quality strings
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89 in files?" truevalue="--store_qual_scores" falsevalue="" checked="False"
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90 help="(--store_qual_scores)" />
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91
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92 <param name="sample_ids" type="text" label="Comma-separated list of samples
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93 ids to be applied to all sequences (optional)" optional="True"
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94 help="It must be one per input file path (used when data is not
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95 multiplexed, --sample_ids)"/>
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96
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97 <param name="store_demultiplexed_fastq" type="boolean" label="Write
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98 demultiplexed fastq files?" truevalue="--store_demultiplexed_fastq"
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99 falsevalue="" checked="False" help="(--store_demultiplexed_fastq)" />
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100
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101 <param name="retain_unassigned_reads" type="boolean" label="Retain
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102 sequences which don’t map to a barcode in the mapping file?"
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103 truevalue="--retain_unassigned_reads" falsevalue="" checked="False"
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104 help="Sample ID will be 'Unassigned' (--retain_unassigned_reads)" />
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105
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106 <param name="max_bad_run_length" type="integer" value="3"
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107 label="Maximum number of consecutive low quality base calls allowed
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108 before truncating a read" help="(-r/--max_bad_run_length)" />
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109
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110 <param name="min_per_read_length_fraction" type="float" value="0.75"
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111 label="Minimum number of consecutive high quality base calls to
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112 include a read (per single end read) as a fraction of the input read
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113 length" help="(-p/--min_per_read_length_fraction)" />
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114
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115 <param name="sequence_max_n" type="integer" value="0"
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116 label="Maximum number of N characters allowed in a sequence to retain
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117 it" help="This is applied after quality trimming, and is total over
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118 combined paired end reads if applicable (-n/--sequence_max_n)" />
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119
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120 <param name="start_seq_id" type="integer" value="0"
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121 label="Start seq_ids as ascending integers beginning with start_seq_id"
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122 help="(-s/--start_seq_id)" />
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123
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124 <param name="rev_comp_barcode" type="boolean" label="Reverse complement
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125 barcode reads before lookup?" truevalue="--rev_comp_barcode"
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126 falsevalue="" checked="False" help="(--rev_comp_barcode)" />
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127
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128 <param name="rev_comp_mapping_barcodes" type="boolean" label="Reverse
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129 complement barcode in mapping before lookup?"
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130 truevalue="--rev_comp_mapping_barcodes" falsevalue="" checked="False"
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131 help="It is useful if barcodes in mapping file are reverse
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132 complements of golay codes (--rev_comp_mapping_barcodes)" />
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133
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134 <param name="rev_comp" type="boolean" label="Reverse omplement sequence
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135 before writing to output file?" truevalue="--rev_comp" falsevalue=""
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136 checked="False" help="(--rev_comp)" />
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137
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138 <param name="phred_quality_threshold" type="integer" value="3"
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139 label="Maximum unacceptable Phred quality score" help="E.g., for
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140 Q20 and better, 19 must be specified (-q/--phred_quality_threshold)" />
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141
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142 <conditional name="barcode_type">
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143 <param name="barcode_selector" type="select" label="Type of barcode"
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144 help="(--barcode_type)">
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145 <option value="hamming_8">hamming_8</option>
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146 <option value="golay_12" selected="true">golay_12</option>
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147 <option value="variable_length">variable_length (disable any barcode correction)</option>
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148 <option value="custom_length">Custom length</option>
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149 <option value="not-barcoded">Data not barcoded</option>
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150 </param>
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151 <when value="hamming_8" />
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152 <when value="golay_12" />
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153 <when value="variable_length" />
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154 <when value="custom_length">
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155 <param name="barcode_length" type="integer" value="4"
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156 label="Barcode length"/>
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157 </when>
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158 <when value="not-barcoded" />
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159 </conditional>
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160
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161 <param name="max_barcode_errors" type="float" value="1.5"
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162 label="Maximum number of errors in barcode"
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163 help="(--max_barcode_errors)" />
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164
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165 <param name="phred_offset" type="select" label="Ascii offset to use when
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166 decoding phred scores" help="(--phred_offset)">
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167 <option value="--phred_offset 33">33</option>
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168 <option value="--phred_offset 64">64</option>
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169 <option value="" selected="true">Automatically determined</option>
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170 </param>
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171 </inputs>
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172
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173 <outputs>
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174 <data name="log" format="txt"
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175 from_work_dir="split_libraries/split_library_log.txt"
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176 label="${tool.name} on ${on_string}: log"/>
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177 <data name="histograms" format="tabular"
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178 from_work_dir="split_libraries/histograms.txt"
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179 label="${tool.name} on ${on_string}: histograms"/>
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180 <data name="seqs" format="fasta"
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181 from_work_dir="split_libraries/seqs.fna"
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182 label="${tool.name} on ${on_string}: sequences"/>
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183 <data name="seqs_qual" format="qual"
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184 from_work_dir="split_libraries/seqs.qual"
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185 label="${tool.name} on ${on_string}: sequence qualities">
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186 <filter>store_qual_scores is True</filter>
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187 </data>
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188 <data name="seqs_fastq" format="fastq"
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189 from_work_dir="split_libraries/seqs.fastq"
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190 label="${tool.name} on ${on_string}: demultiplexed sequences (fastq)">
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191 <filter>store_demultiplexed_fastq is True</filter>
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192 </data>
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193 </outputs>
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194
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195 <tests>
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196 <test>
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197 <param name="input_fastq_files" value="forward_reads.fastq"/>
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198 <param name="input_mapping_files" value="map.tsv"/>
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199 <param name="input_files_barcode_read_fps" value="barcodes.fastq"/>
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200 <param name="store_qual_scores" value="--store_qual_scores" />
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201 <param name="store_demultiplexed_fastq" value="--store_demultiplexed_fastq" />
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202 <param name="retain_unassigned_reads" value=""/>
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203 <param name="max_bad_run_length" value="3"/>
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204 <param name="min_per_read_length_fraction" value="0.75"/>
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205 <param name="sequence_max_n" value="0"/>
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206 <param name="start_seq_id" value="0" />
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207 <param name="rev_comp_barcode" value="" />
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208 <param name="rev_comp_mapping_barcodes" value="" />
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209 <param name="rev_comp" value="" />
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210 <param name="start_seq_id" value="3"/>
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211 <param name="barcode_selector" value="golay_12"/>
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212 <param name="max_barcode_errors" value="1.5"/>
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213 <param name="phred_offset" value="" />
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214
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215 <output name="log" file="split_fastq_libraries_log.txt"/>
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216 <output name="seqs" file="split_fastq_libraries_sequences.fasta"/>
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217 <output name="histograms" file="split_fastq_libraries_histograms.tabular"/>
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218 <output name="histograms" file="split_fastq_libraries_histograms.tabular"/>
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219 <output name="seqs_qual" file="split_fastq_libraries_sequence_qualities.qual"/>
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220 <output name="seqs_fastq" file="split_fastq_libraries_demultiplexed_sequences.fastq"/>
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221 </test>
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222 </tests>
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223
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224 <help><![CDATA[
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225
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226 **What it does**
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227
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228 This tool performs demultiplexing of Fastq sequence data where barcodes and sequences are contained in two separate fastq files (common on Illumina runs).
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229
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230 More information about this tool is available on
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231 `QIIME documentation <http://qiime.org/scripts/split_libraries_fastq.html>`_.
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232 ]]>
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233 </help>
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234
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235 <citations>
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236 <expand macro="citations" />
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237 </citations>
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238
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239 </tool>