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annotate trim_galore.xml @ 6:11962ce40855 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
author bgruening
date Wed, 07 Oct 2015 08:39:59 -0400
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6
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1 <tool id="trim_galore" name="Trim Galore!" version="0.4.0">
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2 <!-- Wrapper compatible with Trim Galore! version 0.4 -->
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3 <description>adaptive quality and adapter trimmer</description>
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4 <macros>
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5 <macro name="adapter_trimming">
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6 <conditional name="trimming">
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7 <param name="trimming_select" type="select" label="Trimming reads?">
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8 <option value="">Automatic detection</option>
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9 <option value="--illumina">Illumina universal</option>
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10 <option value="--nextera">Nextera transposase</option>
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11 <option value="--small_rna">Illumina small RNA adapters</option>
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12 <option value="user">User defined adapter trimming</option>
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13 </param>
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14 <when value="auto"/>
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15 <when value="--illumina"/>
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16 <when value="--nextera"/>
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17 <when value="--small_rna"/>
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18 <when value="user">
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19 <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed off">
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20 <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
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21 </param>
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22 <yield/>
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23 </when>
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24 </conditional>
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25 </macro>
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26 <macro name="paired_adapter_trimming">
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27
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28 <expand macro="adapter_trimming">
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29 <param name="adapter2" type="text" optional="True" value="" label="Adapter sequence to be trimmed off read 2">
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30 <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
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31 </param>
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32 </expand>
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33 <param name="trim1" type="boolean" truevalue="--trim1" falsevalue="" checked="False" label="Trims 1 bp off every read from its 3' end." help="" />
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34 <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 1">
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35 <help>Instructs Trim Galore! to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed.
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36 This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.
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37 (--three_prime_clip_R1)</help>
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38 </param>
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39 <param name="three_prime_clip_R2" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 1">
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40 <help>Instructs Trim Galore! to remove N bp from the 3' end of read 2 after
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41 adapter/quality trimming has been performed. This may remove some unwanted bias from
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42 the 3' end that is not directly related to adapter sequence or basecall quality. (--three_prime_clip_R2)</help>
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43 </param>
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44 </macro>
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45 </macros>
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46 <requirements>
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47 <requirement type="package" version="1.8">cutadapt</requirement>
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48 </requirements>
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49 <version_command interpreter="perl">trim_galore --version</version_command>
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50 <command>
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51 <![CDATA[
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52
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53 ## trim_galore removes .fastq and .fq file extensions of input files.
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54 ## This is essential if Galaxy provides links to files (with real extensions)
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55 ## but that behaviour is causing an inconsistency in output filenaming.
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56 ## We work around this by linking every file to cwd without file extension
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57
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58 #if $singlePaired.sPaired == "single":
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59 ln -s "${singlePaired.input_singles}" ./input_singles;
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60 #elif $singlePaired.sPaired == "paired":
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61 ln -s "${singlePaired.input_mate1}" ./input_mate1;
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62 ln -s "${singlePaired.input_mate2}" ./input_mate2;
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63 #else:
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64 ln -s "${singlePaired.input_mate_pairs.forward}" ./input_mate1;
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65 ln -s "${singlePaired.input_mate_pairs.reverse}" ./input_mate2;
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66 #end if
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67
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68 perl $__tool_directory__/trim_galore
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69
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70 ## we only support fastqsanger
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71 --phred33
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72
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73 #if $params.settingsType == "custom":
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74
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75 ## default 20
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76 --quality $params.quality
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77
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78 ## default 1
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79 --stringency $params.stringency
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80
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81 ## default 0.1
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82 -e $params.error_rate
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83
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84 ## default 20
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85 --length $params.min_length
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86
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87 #if $params.clip_R1:
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88 --clip_R1 $params.clip_R1
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89 #end if
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90
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91 #if $params.clip_R2:
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92 --clip_R2 $params.clip_R2
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93 #end if
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94
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95 #if $params.retain_unpaired.retain_unpaired_select == "retain_unpaired_output":
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96 --retain_unpaired
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97 --length_1 $params.retain_unpaired.length_1
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98 --length_2 $params.retain_unpaired.length_2
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99 #end if
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100
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101 #end if
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102
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103 ## RBBS specific options.
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104 #if $rrbs.settingsType == "custom":
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105 $rrbs.rrbs
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106 $rrbs.non_directional
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107 #end if
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108
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109 --output_dir ./
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110 --suppress_warn
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111
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112 #if $params.settingsType == "custom" and not $params.report:
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113 --no_report_file
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114 #end if
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115
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116 #if $singlePaired.trimming.trimming_select == 'user':
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117 ## default 'AGATCGGAAGAGC'
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118 #if $singlePaired.trimming.adapter.strip() != '':
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119 --adapter $singlePaired.trimming.adapter
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120 #end if
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121 #else:
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122 $singlePaired.trimming.trimming_select
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123 #end if
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124
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125
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126 #if $singlePaired.three_prime_clip_R1:
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127 --three_prime_clip_R1 $singlePaired.three_prime_clip_R1
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128 #end if
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129
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130 #if $singlePaired.sPaired == "single":
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131 ## input sequence
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132 ./input_singles
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133 #else:
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134 --paired
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135
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136 $singlePaired.trim1
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137
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138 #if $singlePaired.trimming.trimming_select == 'user':
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139 #if $singlePaired.trimming.adapter2 and $singlePaired.trimming.adapter2.strip() != '':
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140 --adapter2 $singlePaired.trimming.adapter2
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141 #end if
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142 #end if
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143
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144 #if $singlePaired.three_prime_clip_R2:
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145 --three_prime_clip_R2 $singlePaired.three_prime_clip_R2
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146 #end if
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147
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148 ## input sequences
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149 ./input_mate1
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150 ./input_mate2
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151
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152 #end if
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153
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154 ## Trim Galore! run is finished. Move the report files to the proper place
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155 #if $params.settingsType == "custom" and $params.report:
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156 &&
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157 cat ./*_trimming_report.txt > $report_file;
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158 #end if
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159
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160 ]]>
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161 </command>
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162 <inputs>
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163 <!-- Input Parameters -->
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164 <conditional name="singlePaired">
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165 <param name="sPaired" type="select" label="Is this library paired- or single-end?">
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166 <option value="single">Single-end</option>
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167 <option value="paired">Paired-end</option>
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168 <option value="paired_collection">Paired Collection</option>
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169 </param>
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170 <when value="single">
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171 <param name="input_singles" type="data" format="fastqsanger" label="Reads in FASTQ format" />
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172 <expand macro="adapter_trimming"/>
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173
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174 <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end">
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175 <help>Instructs Trim Galore! to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed.
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176 This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.
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177 (--three_prime_clip_R1)</help>
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178 </param>
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179 </when>
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180 <when value="paired">
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181 <param name="input_mate1" type="data" format="fastqsanger" label="Reads in FASTQ format" />
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182 <param name="input_mate2" type="data" format="fastqsanger" label="Reads in FASTQ format" />
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183 <expand macro="paired_adapter_trimming" />
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184 </when>
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185 <when value="paired_collection">
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186 <param name="input_mate_pairs" format="fastqsanger" type="data_collection" collection_type="paired"
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187 label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
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188 <expand macro="paired_adapter_trimming" />
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189 </when>
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190 </conditional>
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191
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192 <conditional name="params">
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193 <param name="settingsType" type="select" label="Trim Galore! advanced settings" help="You can use the default settings or set custom values for any of Trim Galore!'s parameters.">
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194 <option value="default">Use defaults</option>
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195 <option value="custom">Full parameter list</option>
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196 </param>
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197 <when value="default" />
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198 <!-- Full/advanced params. -->
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199 <when value="custom">
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200 <param name="quality" type="integer" value="20" label="Trim low-quality ends from reads in addition to adapter removal"
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201 help="For more information please see below." />
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202 <param name="stringency" type="integer" value="1" label="Overlap with adapter sequence required to trim a sequence" />
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203 <param name="error_rate" type="float" value="0.1" label="Maximum allowed error rate" />
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204 <param name="min_length" type="integer" value="20" label="Discard reads that became shorter than length INT" />
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205
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206 <param name="clip_R1" type="integer" optional="True" min="0" label="Instructs Trim Galore! to remove INT bp from the 5' end of read 1" />
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207 <param name="clip_R2" type="integer" optional="True" min="0" label="Instructs Trim Galore! to remove INT bp from the 5' end of read 2" />
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208
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209 <param name="report" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Generate a report file" help="" />
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210
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211 <conditional name="retain_unpaired">
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212 <param name="retain_unpaired_select" type="select" label="specify if you would like to retain unpaired reads">
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213 <option value="no_output">Do not output unpaired reads</option>
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214 <option value="retain_unpaired_output">Output unpaired reads</option>
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215 </param>
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216 <when value="no_output" />
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217 <!-- Output params. -->
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218 <when value="retain_unpaired_output">
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219 <param name="length_1" type="integer" value="35" label="Unpaired single-end read length cutoff needed for read 1 to be written" />
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220 <param name="length_2" type="integer" value="35" label="Unpaired single-end read length cutoff needed for read 2 to be written" />
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221 </when> <!-- output -->
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222 </conditional> <!-- retain_unpaired -->
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223
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224 </when> <!-- full -->
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225 </conditional> <!-- params -->
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226
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227 <conditional name="rrbs">
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228 <param name="settingsType" type="select" label="RRBS specific settings">
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229 <option value="default">Use defaults (no RRBS)</option>
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230 <option value="custom">Full parameter list</option>
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231 </param>
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232 <when value="default" />
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233 <!-- Full/advanced params. -->
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234 <when value="custom">
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235 <param name="rrbs" type="boolean" truevalue="--rrbs" falsevalue="" checked="True"
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236 label="Specifies that the input file was an MspI digested RRBS sample" />
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237 <param name="non_directional" type="boolean" truevalue="--non_directional" falsevalue="" checked="False"
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238 label="Selecting this option for non-directional RRBS libraries" />
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239 </when> <!-- full -->
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240 </conditional> <!-- params -->
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241
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242 </inputs>
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243 <outputs>
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244 <data format="fastqsanger" name="trimmed_reads_single" from_work_dir="input_singles_trimmed.fq" label="${tool.name} on ${on_string}: trimmed reads">
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245 <filter>singlePaired['sPaired'] == "single"</filter>
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246 </data>
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247
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248 <collection name="trimmed_reads_paired_collection" type="paired" label="${tool.name} on ${on_string}: paired reads">
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249 <data name="forward" format="fastqsanger" from_work_dir="input_mate1_val_1.fq" />
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250 <data name="reverse" format="fastqsanger" from_work_dir="input_mate2_val_2.fq" />
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251 <filter>singlePaired['sPaired'] == "paired_collection"</filter>
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252 </collection>
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253
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254 <collection name="trimmed_reads_unpaired_collection" type="paired" label="${tool.name} on ${on_string}: unpaired reads">
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255 <data name="forward" format="fastqsanger" from_work_dir="input_mate1_unpaired_1.fq" />
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256 <data name="reverse" format="fastqsanger" from_work_dir="input_mate2_unpaired_2.fq" />
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257 <filter>params['settingsType'] == "custom"</filter>
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258 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
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259 <filter>singlePaired['sPaired'] == "paired_collection"</filter>
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260 </collection>
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261
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262 <data format="fastqsanger" name="trimmed_reads_pair1" from_work_dir="input_mate1_val_1.fq"
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263 label="${tool.name} on ${on_string}: trimmed reads pair 1">
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264 <filter>singlePaired['sPaired'] == "paired"</filter>
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265 </data>
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266
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267 <data format="fastqsanger" name="trimmed_reads_pair2" from_work_dir="input_mate2_val_2.fq"
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268 label="${tool.name} on ${on_string}: trimmed reads pair 2">
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269 <filter>singlePaired['sPaired'] == "paired"</filter>
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270 </data>
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271
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272 <data format="fastqsanger" name="unpaired_reads_1" from_work_dir="input_mate1_val_1.fq"
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273 label="${tool.name} on ${on_string}: unpaired reads (1)">
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274 <filter>params['settingsType'] == "custom"</filter>
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275 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
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276 <filter>singlePaired['sPaired'] == "paired"</filter>
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277 </data>
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278
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279 <data format="fastqsanger" name="unpaired_reads_2" from_work_dir="input_mate2_val_2.fq"
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280 label="${tool.name} on ${on_string}: unpaired reads (2)">
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281 <filter>params['settingsType'] == "custom"</filter>
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282 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
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283 <filter>singlePaired['sPaired'] == "paired"</filter>
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284 </data>
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285 <data format="txt" name="report_file" label="${tool.name} on ${on_string}: report file">
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286 <filter>params['settingsType'] == "custom"</filter>
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287 <filter>params['report'] == True</filter>
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288 </data>
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289
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290 </outputs>
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291 <tests>
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292 <test>
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293 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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294 <param name="sPaired" value="single" />
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295 <param name="settingsType" value="custom" />
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296 <param name="report" value="true" />
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297 <output name="trimmed_reads_single" file="sanger_full_range_results1.fastqsanger" ftype="fastqsanger"/>
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298 <output name="report_file" file="sanger_full_range_report_results1.txt" ftype="txt" lines_diff="2" />
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299 </test>
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300
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301 <test>
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302 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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303 <param name="sPaired" value="single" />
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304 <param name="trimming_select" value="--illumina" />
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305 <output name="trimmed_reads_single" file="sanger_full_range_results2.fastqsanger" ftype="fastqsanger"/>
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306 </test>
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307
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308 <test>
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309 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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310 <param name="sPaired" value="single" />
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311 <param name="adapter" value="AAAGAGC" />
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312 <output name="trimmed_reads_single" file="sanger_full_range_results3.fastqsanger" ftype="fastqsanger"/>
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313 </test>
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314
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315 <test>
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316 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
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317 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
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318 <param name="sPaired" value="paired" />
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319 <param name="settingsType" value="custom" />
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320 <param name="report" value="true" />
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321 <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastqsanger" ftype="fastqsanger"/>
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322 <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastqsanger" ftype="fastqsanger"/>
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323 <output name="report_file" file="paired_example_results2.txt" ftype="txt" lines_diff="8" />
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324 </test>
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325
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326 <test>
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327 <param name="input_mate_pairs">
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328 <collection type="paired">
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329 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
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330 <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
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331 </collection>
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332 </param>
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333
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334 <param name="sPaired" value="paired_collection" />
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335 <param name="settingsType" value="custom" />
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336 <param name="report" value="true" />
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337 <param name="retain_unpaired_select" value="retain_unpaired_output" />
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338
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339 <output name="report_file" file="paired_collection_example_results3.txt" ftype="txt" lines_diff="8" />
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340
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341 <output_collection name="trimmed_reads_paired_collection" type="paired">
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342 <element name="forward" file="paired_collection_example_pair1_results3.fastqsanger" ftype="fastqsanger"/>
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343 <element name="reverse" file="paired_collection_example_pair2_results3.fastqsanger" ftype="fastqsanger"/>
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344 </output_collection>
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345
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346 <output_collection name="trimmed_reads_unpaired_collection" type="paired">
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347 <element name="forward" file="paired_collection_example_unpair1_results3.fastqsanger" ftype="fastqsanger"/>
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348 <element name="reverse" file="paired_collection_example_unpair2_results3.fastqsanger" ftype="fastqsanger"/>
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349 </output_collection>
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350
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351 </test>
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352 </tests>
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353 <help>
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354 <![CDATA[
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355 **What it does**
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356
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357 `Trim Galore!`_ is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). It's main features are:
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358
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359 * For adapter trimming, Trim Galore! uses the first 13 bp of Illumina standard adapters ('AGATCGGAAGAGC') by default (suitable for both ends of paired-end libraries), but accepts other adapter sequence, too
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360 * For MspI-digested RRBS libraries, Trim Galore! performs quality and adapter trimming in two subsequent steps. This allows it to remove 2 additional bases that contain a cytosine which was artificially introduced in the end-repair step during the library preparation
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361 * For any kind of FASTQ file other than MspI-digested RRBS, Trim Galore! can perform single-pass adapter and quality trimming
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362 * The Phred quality of basecalls and the stringency for adapter removal can be specified individually
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363 * Trim Galore! can remove sequences if they become too short during the trimming process. For paired-end files Trim Galore! removes entire sequence pairs if one (or both) of the two reads became shorter than the set length cutoff. Reads of a read-pair that are longer than a given threshold but for which the partner read has become too short can optionally be written out to single-end files. This ensures that the information of a read pair is not lost entirely if only one read is of good quality
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364 * Trim Galore! can trim paired-end files by 1 additional bp from the 3' end of all reads to avoid problems with invalid alignments with Bowtie 1
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365
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366 .. _Trim Galore!: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
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367
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368 It is developed by Felix Krueger at the Babraham Institute.
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369 ]]>
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370 </help>
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371 <citations></citations>
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372 </tool>