Mercurial > repos > jjohnson > fastq_mcf
annotate fastq-mcf.xml @ 1:b61f1466ce8f default tip
Add tool_dependencies.xml and test case
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 01 Apr 2013 10:28:17 -0500 |
| parents | 217aedbdd0d0 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="fastq_mcf" name="FastqMcf" version="1.0"> |
| 2 <description>sequence quality filtering and clipping</description> | |
| 3 <requirements> | |
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Add tool_dependencies.xml and test case
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4 <requirement type="package" version="1.1.2-484">ea-utils</requirement> |
| 0 | 5 </requirements> |
| 6 <version_string>fastq-mcf -V</version_string> | |
| 7 <command>fastq-mcf | |
| 8 #if $trimming.choice == 'disable': | |
| 9 -0 | |
| 10 #elif $trimming.choice == 'user_set': | |
| 11 #if len($trimming.scale.__str__) > 0 | |
| 12 -s $trimming.scale | |
| 13 #end if | |
| 14 #if len($trimming.minpct.__str__) > 0 | |
| 15 -t $trimming.minpct | |
| 16 #end if | |
| 17 #if len($trimming.nmin.__str__) > 0 | |
| 18 -m $trimming.nmin | |
| 19 #end if | |
| 20 #if len($trimming.pctdiff.__str__) > 0 | |
| 21 -p $trimming.pctdiff | |
| 22 #end if | |
| 23 #if len($trimming.nmax.__str__) > 0 | |
| 24 -L $trimming.nmax | |
| 25 #end if | |
| 26 #if len($trimming.nkeep.__str__) > 0 | |
| 27 -l $trimming.nkeep | |
| 28 #end if | |
| 29 #if len($trimming.skewpct.__str__) > 0 | |
| 30 -k $trimming.skewpct | |
| 31 #end if | |
| 32 #if len($trimming.qthr.__str__) > 0 | |
| 33 -q $trimming.qthr | |
| 34 #end if | |
| 35 #if len($trimming.qwin.__str__) > 0 | |
| 36 -w $trimming.qwin | |
| 37 #end if | |
| 38 #if len($trimming.pctns.__str__) > 0 | |
| 39 -x $trimming.pctns | |
| 40 #end if | |
| 41 #if len($trimming.sampcnt.__str__) > 0 | |
| 42 -s $trimming.sampcnt | |
| 43 #end if | |
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44 #if len($trimming.ilv3.__str__.strip()) > 0 |
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b61f1466ce8f
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parents:
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45 -$trimming.ilv3 |
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46 #end if |
| 0 | 47 $trimming.rmns |
| 48 #end if | |
| 49 #if $noclip == True : | |
| 50 $noclip | |
| 51 #else : | |
| 52 -o $reads_out | |
| 53 #if $mates.__str__ != 'None' : | |
| 54 -o $mates_out | |
| 55 #end if | |
| 56 #end if | |
| 57 $adpaters | |
| 58 $reads | |
| 59 #if $mates.__str__ != 'None' : | |
| 60 $mates | |
| 61 #end if | |
| 62 > $log | |
| 63 </command> | |
| 64 <inputs> | |
| 65 <param name="adpaters" type="data" format="fasta" label="A fasta formatted adapter list" /> | |
| 66 <param name="reads" type="data" format="fastqsanger,fastqillumina" label="Reads: single or Left-hand of Paired End Reads" /> | |
| 67 <param name="mates" type="data" format="fastqsanger,fastqillumina" optional="true" label="Right-hand mates for Paired End Reads" /> | |
| 68 <!-- | |
| 69 -s N.N Log scale for clip pct to threshold (2.5) | |
| 70 -t N % occurance threshold before clipping (0.25) | |
| 71 -m N Minimum clip length, overrides scaled auto (1) | |
| 72 -p N Maximum adapter difference percentage (20) | |
| 73 -l N Minimum remaining sequence length (15) | |
| 74 -L N Maximum sequence length (none) | |
| 75 -k N sKew percentage causing trimming (2) | |
| 76 -q N quality threshold causing trimming (10) | |
| 77 -f force output, even if not much will be done | |
| 78 -0 Set all trimming parameters to zero | |
| 79 -U|u Force disable/enable illumina PF filtering | |
| 80 -P N phred-scale (64) | |
| 81 -x N 'N' (Bad read) percentage causing trimming (10) | |
| 82 -R Don't remove N's from the fronts/ends of reads | |
| 83 -n Don't clip, just output what would be done | |
| 84 -C N Number of reads to use for subsampling (200000) | |
| 85 -d Output lots of random debugging stuff | |
| 86 --> | |
| 87 | |
| 88 | |
| 89 <conditional name="trimming"> | |
| 90 <param name="choice" type="select" label="Trimming Options"> | |
| 91 <option value="defaults">Use Defaults</option> | |
| 92 <option value="user_set">Set Values</option> | |
| 93 <option value="disable">Set all trimming parameters to zero</option> | |
| 94 </param> | |
| 95 <when value="defaults"/> | |
| 96 <when value="disable"/> | |
| 97 <when value="user_set"> | |
| 98 <param name="sampcnt" type="integer" optional="true" label="-C Number of reads to use for subsampling (100000)"> | |
| 99 </param> | |
| 100 <param name="scale" type="float" optional="true" label="-s N.N Log scale for clip pct to threshold (2.5)"> | |
| 101 </param> | |
| 102 <param name="minpct" type="float" optional="true" label="-t % occurance threshold before clipping (0.25)"> | |
| 103 </param> | |
| 104 <param name="nmin" type="integer" optional="true" label="-m Minimum clip length, overrides scaled auto (1)"> | |
| 105 </param> | |
| 106 <param name="pctdiff" type="integer" optional="true" label="-p Maximum adapter difference percentage (20)"> | |
| 107 </param> | |
| 108 | |
| 109 <param name="nmax" type="integer" optional="true" label="-L Maximum sequence length (none)"> | |
| 110 </param> | |
| 111 <param name="nkeep" type="integer" optional="true" label="-l Minimum remaining sequence length (15)"> | |
| 112 </param> | |
| 113 <param name="skewpct" type="float" optional="true" label="-k sKew percentage causing trimming (2)"> | |
| 114 </param> | |
| 115 <param name="qthr" type="integer" optional="true" label="-q quality threshold causing trimming (7)" | |
| 116 help="remove end of-read with quality < threshold"> | |
| 117 </param> | |
| 118 <param name="qwin" type="integer" optional="true" label="-w mean quality threshold causing trimming (1)" | |
| 119 help="remove end of read with mean quality < threshold"> | |
| 120 </param> | |
| 121 <param name="pctns" type="float" optional="true" label="-x 'N' (Bad read) percentage causing trimming (10)"> | |
| 122 </param> | |
| 123 <param name="rmns" type="boolean" truevalue="-R" falsevalue="" checked="false" label="-R Don't remove N's from the fronts/ends of reads"/> | |
| 124 <param name="ilv3" type="select" label="illumina PF filtering"> | |
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Add tool_dependencies.xml and test case
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parents:
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125 <option value="">Default</option> |
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126 <option value="U">Disable illumina PF filtering</option> |
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parents:
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changeset
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127 <option value="u">Enable illumina PF filtering</option> |
| 0 | 128 </param> |
| 129 </when> | |
| 130 </conditional> | |
| 131 | |
| 132 | |
| 133 <param name="phred" type="integer" optional="true" label="-P phred-scale (64)" help="Default is to determine automatically"> | |
| 134 </param> | |
| 135 | |
| 136 <param name="noclip" type="boolean" truevalue="-n" falsevalue="" checked="false" label="-n Don't clip, just output what would be done"/> | |
| 137 | |
| 138 </inputs> | |
| 139 <outputs> | |
| 140 <data name="log" format="txt" label="${tool.name} on ${on_string}: log"/> | |
| 141 <data name="reads_out" format_source="reads" label="${tool.name} on ${on_string}: reads"> | |
| 142 <filter>noclip == False</filter> | |
| 143 </data> | |
| 144 <data name="mates_out" format_source="mates" label="${tool.name} on ${on_string}: mates"> | |
| 145 <filter>(noclip == False and mates != None)</filter> | |
| 146 </data> | |
| 147 </outputs> | |
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148 <stdio> |
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149 <exit_code range="1:" level="fatal" description="Error" /> |
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150 </stdio> |
| 0 | 151 <tests> |
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parents:
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152 <test> |
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parents:
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153 <param name="adpaters" ftype="fasta" value="adapters.fa" /> |
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154 <param name="reads" ftype="fastqillumina" value="test_mcf_reads.fq" /> |
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155 <param name="mates" ftype="fastqillumina" value="test_mcf_mates.fq" /> |
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156 <param name="choice" value="user_set" /> |
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157 <param name="nkeep" value="16" /> |
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158 <param name="qthr" value="15" /> |
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159 <param name="qwin" value="5" /> |
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160 <param name="pctns" value="10" /> |
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161 <param name="ilv3" value="u" /> |
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162 <param name="phred" value="33" /> |
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163 <output name="reads_out" file="testout_mcf_reads.fq" /> |
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164 <output name="mates_out" file="testout_mcf_mates.fq" /> |
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165 </test> |
| 0 | 166 </tests> |
| 167 <help> | |
| 168 **What it does** | |
| 169 | |
| 170 fastq-mcf_ attempts to: | |
| 171 | |
| 172 Detect and remove sequencing adapters and primers | |
| 173 Detect limited skewing at the ends of reads and clip | |
| 174 Detect poor quality at the ends of reads and clip | |
| 175 Detect N's, and remove from ends | |
| 176 Remove reads with CASAVA 'Y' flag (purity filtering) | |
| 177 Discard sequences that are too short after all of the above | |
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178 |
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179 |
| 0 | 180 Keep multiple mate-reads in sync while doing all of the above |
| 181 | |
| 182 .. _fastq-mcf: http://code.google.com/p/ea-utils/wiki/FastqMcf | |
| 183 ----- | |
| 184 | |
| 185 **Input** | |
| 186 | |
| 187 Fasta file of adapter sequences, for example:: | |
| 188 | |
| 189 > Genomic_DNA_oligonucleotide_sequences_Adapters_F | |
| 190 GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG | |
| 191 > Genomic_DNA_oligonucleotide_sequences_Adapters_R | |
| 192 ACACTCTTTCCCTACACGACGCTCTTCCGATCT | |
| 193 > Genomic_DNA_Sequencing_Primer | |
| 194 ACACTCTTTCCCTACACGACGCTCTTCCGATCT | |
| 195 | |
| 196 | |
| 197 | |
| 198 Reads or Left-hand mates, for example:: | |
| 199 | |
| 200 @1539:931/1 | |
| 201 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG | |
| 202 +1539:931/1 | |
| 203 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB | |
| 204 | |
| 205 Right-hand mates, for example:: | |
| 206 | |
| 207 @1539:931/2 | |
| 208 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT | |
| 209 +1539:931/2 | |
| 210 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB | |
| 211 | |
| 212 ----- | |
| 213 | |
| 214 **Output** | |
| 215 | |
| 216 A log file | |
| 217 | |
| 218 A trimmed fastq of the reads | |
| 219 | |
| 220 A trimmed fastq of the mates | |
| 221 | |
| 222 | |
| 223 | |
| 224 </help> | |
| 225 </tool> |