annotate macros.xml @ 0:40c86e14b674 draft

Uploaded first version of tagdust
author brenninc
date Mon, 09 May 2016 04:08:01 -0400
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1 <?xml version="1.0"?>
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2 <macros>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="2.31">tagdust</requirement>
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6 </requirements>
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7 </xml>
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8 <xml name="version_command">
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9 <version_command>tagdust --version | head -n 1 | awk '{ print $2 }'</version_command>
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10 </xml>
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11 <xml name="stdio">
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12 <stdio>
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13 <exit_code range="1:" level="fatal" description="Error" />
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14 </stdio>
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15 </xml>
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16 <token name="@cat-archiecture@">
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17 echo using architecture ;
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18 cat $architecture.fields.path ;
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19 echo ;
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20 </token>
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21 <token name="@tagdust-call-minus-files@">
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22 mkdir output ;
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23 tagdust -t\${GALAXY_SLOTS:-4} -o output/data
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24 -arch $architecture.fields.path
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25 #if $reference_source.reference_source_selector=='history':
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26 -ref $reference_source.ref_file
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27 #end if
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28 #if $reference_source.reference_source_selector=='cached':
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29 -ref $reference_source.ref_path.fields.path
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30 #end if
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31 </token>
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32 <token name="@ls_and_barcode@">
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33 echo files in output folder ;
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34 ls -al output ;
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35 #if $include.barcode_files=="yes"
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36 #if $architecture.fields.barcode=="yes"
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37 cd output ;
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38 ls *_BC_* > $barcode_files
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39 #else
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40 echo Selected architecture not expected to generate any barcode files > $barcode_files ;
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41 echo To avoid this output set Choose to find the barcode files to No >> $barcode_files ;
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42 #end if
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43 #else
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44 #if $architecture.fields.barcode=="yes"
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45 echo ;
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46 echo Tagdust not included in output at users request! ;
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47 echo To get then set Choose to find the barcode files to Yes and run the tool again ;
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48 #end if
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49 #end if
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50 </token>
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51 <xml name="architecture">
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52 <param name="architecture" type="select" label="Using architecture">
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53 <options from_data_table="tagdust_architecture"/>
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54 <validator type="no_options" message="No architecture found"/>
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55 <!--filter name="barcode" value="yes" column="3"/-->
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56 </param>
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57 </xml>
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58 <xml name="reference_source">
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59 <conditional name="reference_source">
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60 <param name="reference_source_selector" type="select" label="Choose the source for the reference fasta (If any)">
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61 <option value="none" selected="true">Do not include a reference fasta</option>
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62 <option value="cached">Locally cached</option>
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63 <option value="history">History</option>
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64 </param>
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65 <when value="none"/>
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66 <when value="cached">
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67 <param name="ref_path" type="select" label="Using reference fasta">
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68 <options from_data_table="all_fasta"/>
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69 <validator type="no_options" message="A built-in reference fasta is not available for the build associated with the selected input file"/>
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70 </param>
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71 </when>
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72 <when value="history">
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73 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
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74 </when>
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75 </conditional>
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76 </xml>
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77 <xml name="include_barcode_file">
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78 <conditional name="include">
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79 <param name="barcode_files" type="select" label="Choose to find the barcode files (If any)">
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80 <option value="yes" selected="true">Yes. Look for possible barcode separated files.</option>
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81 <option value="no" >No. Ignores all barcode files even if these are generated.</option>
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82 </param>
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83 <when value="yes"/>
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84 <when value="no"/>
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85 </conditional>
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86 </xml>
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87 <xml name="output_barcode">
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88 <data format="txt" name="barcode_files" label="Tagdust barcoded reads.">
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89 <discover_datasets pattern="data_BC_(?P&lt;designation&gt;.+)\.fq" ext="fastq" directory="output" visible="true" />
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90 <filter>(include['barcode_files']=='yes')</filter>
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91 </data>
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92 </xml>
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93 <token name="@tool-documentation@">
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94 <![CDATA[
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95
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96 Note: Output from Architecture with could have a Barcode HMM building block choose to find the barcode files.
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97 ....If no barcode files are found this will simply be empty.
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98 ....You may have refresh the history for all barcode files to show.
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99
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100 Please contact the admin to add an architecture / HMM building blocks.
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101 (There is Data Manager that they can use)
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102
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103 ]]>
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104 </token>
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105 <token name="@tagdust-documentation@">
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106 <![CDATA[
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107 ====
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108
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109 Taken from The TagDust2 Manual http://tagdust.sourceforge.net (part of Version 2_31 download)
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110
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111 Raw sequences produced by next generation sequencing (NGS) machines can contain adapter, linker,
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112 barcode and fingerprint sequences. TagDust2 is a program to extract and correctly label the sequences
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113 to be mapped in downstream pipelines.
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114 TagDust allows users to specify the expected architecture of a read and converts it into a hidden
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115 Markov model. The latter can assign sequences to a particular barcode (or index) even in the presence
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116 of sequencing errors. Sequences not matching the architecture (primer dimers, contaminants etc.) are
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117 automatically discarded
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118
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119 TagDust requires an input file containing sequences and a user defined HMM architecture used to ex-
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120 tract the reads. The architecture is composed of a selection of pre-defined building blocks representing
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121 indices, barcodes, spacers and other sequences one might encounter in the raw output of a sequenced
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122 sample.
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123
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124 HMM Building Blocks
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125
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126 TagDust comes with a set of pre-defined HMM building blocks. Each includes a silent state at the
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127 beginning and end used to link blocks together. Each block is specified by a unique letter following
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128 by a colon and some information about the sequence.
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129
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130 Read
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131 Segment modeling the read.
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132 Code: R:N
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133
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134 Optional
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135 Segment modeling an optional single or short stretch of nucleotides.
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136 Code: O:N
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137
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138 G addition
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139 Segment modeling the occasional addition of guanines to the reads.
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140 (89.3% chance of a single G , 19.5% chance of 2 Gs..).
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141 Code: G:G
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142
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143 Barcode or Index
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144 Segment modeling a set of barcode sequences. For each sequence a separate HMM is created. The
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145 barcode sequences must be given as a comma separated list. A null model of the same length as the
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146 barcode is automatically added and initialized to the background nucleotide frequencies.
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147 Code: B:GTA,AAC
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148
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149 Fingerprint or Unique Molecular Identifier - UMI
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150 Segment modeling a fingerprint (or unique molecular identifiers). Insertions and deletions are by
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151 default not allowed within a fingerprint segment.
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152 Code: F:NNN
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153
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154 Spacer
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155 Segment modeling a pre-defined sequence.
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156 Code: S:GTA
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157
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158 Partial
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159 This segment is used to model sequences that may only be partially present at the 5‘ or 3‘ end of
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160 the read. The transition probabilities (orange and blue) are set automatically based on the length
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161 distribution of exactly matching adapters.
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162 Code: P:CCTTAA
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163 ]]>
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164 </token>
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165 <xml name="citations">
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166 <citations>
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167 <citation type="bibtex">
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168 @misc{
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169 TagDust,
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170 author = {Timo Lassmann},
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171 title = {TagDust on sourceforge},
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172 url = {http://tagdust.sourceforge.net/}
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173 }
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174 </citation>
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175 <citation type="doi">10.1093/bioinformatics/btp527</citation>
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176 <citation type="doi">10.1186/s12859-015-0454-y</citation>
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177 </citations>
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178 </xml>
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179 </macros>