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1 <tool id="fastq_mcf" name="FastqMcf" version="1.0">
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2 <description>sequence quality filtering and clipping</description>
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3 <requirements>
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4 <requirement type="binary">fastq-mcf</requirement>
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5 </requirements>
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6 <version_string>fastq-mcf -V</version_string>
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7 <command>fastq-mcf
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8 #if $trimming.choice == 'disable':
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9 -0
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10 #elif $trimming.choice == 'user_set':
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11 #if len($trimming.scale.__str__) > 0
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12 -s $trimming.scale
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13 #end if
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14 #if len($trimming.minpct.__str__) > 0
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15 -t $trimming.minpct
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16 #end if
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17 #if len($trimming.nmin.__str__) > 0
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18 -m $trimming.nmin
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19 #end if
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20 #if len($trimming.pctdiff.__str__) > 0
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21 -p $trimming.pctdiff
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22 #end if
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23 #if len($trimming.nmax.__str__) > 0
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24 -L $trimming.nmax
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25 #end if
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26 #if len($trimming.nkeep.__str__) > 0
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27 -l $trimming.nkeep
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28 #end if
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29 #if len($trimming.skewpct.__str__) > 0
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30 -k $trimming.skewpct
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31 #end if
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32 #if len($trimming.qthr.__str__) > 0
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33 -q $trimming.qthr
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34 #end if
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35 #if len($trimming.qwin.__str__) > 0
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36 -w $trimming.qwin
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37 #end if
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38 #if len($trimming.pctns.__str__) > 0
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39 -x $trimming.pctns
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40 #end if
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41 #if len($trimming.sampcnt.__str__) > 0
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42 -s $trimming.sampcnt
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43 #end if
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44 $trimming.ilv3
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45 $trimming.rmns
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46 #end if
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47 #if $noclip == True :
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48 $noclip
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49 #else :
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50 -o $reads_out
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51 #if $mates.__str__ != 'None' :
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52 -o $mates_out
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53 #end if
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54 #end if
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55 $adpaters
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56 $reads
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57 #if $mates.__str__ != 'None' :
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58 $mates
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59 #end if
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60 > $log
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61 </command>
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62 <inputs>
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63 <param name="adpaters" type="data" format="fasta" label="A fasta formatted adapter list" />
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64 <param name="reads" type="data" format="fastqsanger,fastqillumina" label="Reads: single or Left-hand of Paired End Reads" />
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65 <param name="mates" type="data" format="fastqsanger,fastqillumina" optional="true" label="Right-hand mates for Paired End Reads" />
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66 <!--
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67 -s N.N Log scale for clip pct to threshold (2.5)
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68 -t N % occurance threshold before clipping (0.25)
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69 -m N Minimum clip length, overrides scaled auto (1)
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70 -p N Maximum adapter difference percentage (20)
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71 -l N Minimum remaining sequence length (15)
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72 -L N Maximum sequence length (none)
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73 -k N sKew percentage causing trimming (2)
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74 -q N quality threshold causing trimming (10)
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75 -f force output, even if not much will be done
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76 -0 Set all trimming parameters to zero
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77 -U|u Force disable/enable illumina PF filtering
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78 -P N phred-scale (64)
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79 -x N 'N' (Bad read) percentage causing trimming (10)
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80 -R Don't remove N's from the fronts/ends of reads
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81 -n Don't clip, just output what would be done
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82 -C N Number of reads to use for subsampling (200000)
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83 -d Output lots of random debugging stuff
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84 -->
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85
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86
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87 <conditional name="trimming">
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88 <param name="choice" type="select" label="Trimming Options">
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89 <option value="defaults">Use Defaults</option>
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90 <option value="user_set">Set Values</option>
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91 <option value="disable">Set all trimming parameters to zero</option>
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92 </param>
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93 <when value="defaults"/>
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94 <when value="disable"/>
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95 <when value="user_set">
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96 <param name="sampcnt" type="integer" optional="true" label="-C Number of reads to use for subsampling (100000)">
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97 </param>
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98 <param name="scale" type="float" optional="true" label="-s N.N Log scale for clip pct to threshold (2.5)">
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99 </param>
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100 <param name="minpct" type="float" optional="true" label="-t % occurance threshold before clipping (0.25)">
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101 </param>
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102 <param name="nmin" type="integer" optional="true" label="-m Minimum clip length, overrides scaled auto (1)">
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103 </param>
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104 <param name="pctdiff" type="integer" optional="true" label="-p Maximum adapter difference percentage (20)">
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105 </param>
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106
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107 <param name="nmax" type="integer" optional="true" label="-L Maximum sequence length (none)">
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108 </param>
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109 <param name="nkeep" type="integer" optional="true" label="-l Minimum remaining sequence length (15)">
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110 </param>
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111 <param name="skewpct" type="float" optional="true" label="-k sKew percentage causing trimming (2)">
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112 </param>
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113 <param name="qthr" type="integer" optional="true" label="-q quality threshold causing trimming (7)"
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114 help="remove end of-read with quality < threshold">
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115 </param>
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116 <param name="qwin" type="integer" optional="true" label="-w mean quality threshold causing trimming (1)"
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117 help="remove end of read with mean quality < threshold">
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118 </param>
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119 <param name="pctns" type="float" optional="true" label="-x 'N' (Bad read) percentage causing trimming (10)">
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120 </param>
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121 <param name="rmns" type="boolean" truevalue="-R" falsevalue="" checked="false" label="-R Don't remove N's from the fronts/ends of reads"/>
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122 <param name="ilv3" type="select" label="illumina PF filtering">
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123 <option value=" ">Default</option>
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124 <option value="-U">Disable illumina PF filtering</option>
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125 <option value="-u">Enable illumina PF filtering</option>
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126 </param>
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127 </when>
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128 </conditional>
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129
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130
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131 <param name="phred" type="integer" optional="true" label="-P phred-scale (64)" help="Default is to determine automatically">
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132 </param>
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133
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134 <param name="noclip" type="boolean" truevalue="-n" falsevalue="" checked="false" label="-n Don't clip, just output what would be done"/>
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135
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136 </inputs>
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137 <outputs>
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138 <data name="log" format="txt" label="${tool.name} on ${on_string}: log"/>
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139 <data name="reads_out" format_source="reads" label="${tool.name} on ${on_string}: reads">
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140 <filter>noclip == False</filter>
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141 </data>
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142 <data name="mates_out" format_source="mates" label="${tool.name} on ${on_string}: mates">
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143 <filter>(noclip == False and mates != None)</filter>
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144 </data>
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145 </outputs>
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146 <tests>
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147 </tests>
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148 <help>
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149 **What it does**
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150
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151 fastq-mcf_ attempts to:
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152
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153 Detect and remove sequencing adapters and primers
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154 Detect limited skewing at the ends of reads and clip
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155 Detect poor quality at the ends of reads and clip
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156 Detect N's, and remove from ends
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157 Remove reads with CASAVA 'Y' flag (purity filtering)
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158 Discard sequences that are too short after all of the above
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159 Keep multiple mate-reads in sync while doing all of the above
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160
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161 .. _fastq-mcf: http://code.google.com/p/ea-utils/wiki/FastqMcf
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162 -----
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163
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164 **Input**
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165
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166 Fasta file of adapter sequences, for example::
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167
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168 > Genomic_DNA_oligonucleotide_sequences_Adapters_F
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169 GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG
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170 > Genomic_DNA_oligonucleotide_sequences_Adapters_R
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171 ACACTCTTTCCCTACACGACGCTCTTCCGATCT
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172 > Genomic_DNA_Sequencing_Primer
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173 ACACTCTTTCCCTACACGACGCTCTTCCGATCT
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174
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175
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176
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177 Reads or Left-hand mates, for example::
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178
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179 @1539:931/1
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180 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
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181 +1539:931/1
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182 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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183
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184 Right-hand mates, for example::
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185
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186 @1539:931/2
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187 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
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188 +1539:931/2
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189 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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190
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191 -----
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192
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193 **Output**
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194
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195 A log file
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196
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197 A trimmed fastq of the reads
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198
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199 A trimmed fastq of the mates
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200
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201
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202
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203 </help>
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204 </tool>
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