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comparison fastq-mcf.xml @ 0:217aedbdd0d0

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author jjohnson
date Tue, 13 Mar 2012 14:44:46 -0400
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1 <tool id="fastq_mcf" name="FastqMcf" version="1.0">
2 <description>sequence quality filtering and clipping</description>
3 <requirements>
4 <requirement type="binary">fastq-mcf</requirement>
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
44 $trimming.ilv3
45 $trimming.rmns
46 #end if
47 #if $noclip == True :
48 $noclip
49 #else :
50 -o $reads_out
51 #if $mates.__str__ != 'None' :
52 -o $mates_out
53 #end if
54 #end if
55 $adpaters
56 $reads
57 #if $mates.__str__ != 'None' :
58 $mates
59 #end if
60 > $log
61 </command>
62 <inputs>
63 <param name="adpaters" type="data" format="fasta" label="A fasta formatted adapter list" />
64 <param name="reads" type="data" format="fastqsanger,fastqillumina" label="Reads: single or Left-hand of Paired End Reads" />
65 <param name="mates" type="data" format="fastqsanger,fastqillumina" optional="true" label="Right-hand mates for Paired End Reads" />
66 <!--
67 -s N.N Log scale for clip pct to threshold (2.5)
68 -t N % occurance threshold before clipping (0.25)
69 -m N Minimum clip length, overrides scaled auto (1)
70 -p N Maximum adapter difference percentage (20)
71 -l N Minimum remaining sequence length (15)
72 -L N Maximum sequence length (none)
73 -k N sKew percentage causing trimming (2)
74 -q N quality threshold causing trimming (10)
75 -f force output, even if not much will be done
76 -0 Set all trimming parameters to zero
77 -U|u Force disable/enable illumina PF filtering
78 -P N phred-scale (64)
79 -x N 'N' (Bad read) percentage causing trimming (10)
80 -R Don't remove N's from the fronts/ends of reads
81 -n Don't clip, just output what would be done
82 -C N Number of reads to use for subsampling (200000)
83 -d Output lots of random debugging stuff
84 -->
85
86
87 <conditional name="trimming">
88 <param name="choice" type="select" label="Trimming Options">
89 <option value="defaults">Use Defaults</option>
90 <option value="user_set">Set Values</option>
91 <option value="disable">Set all trimming parameters to zero</option>
92 </param>
93 <when value="defaults"/>
94 <when value="disable"/>
95 <when value="user_set">
96 <param name="sampcnt" type="integer" optional="true" label="-C Number of reads to use for subsampling (100000)">
97 </param>
98 <param name="scale" type="float" optional="true" label="-s N.N Log scale for clip pct to threshold (2.5)">
99 </param>
100 <param name="minpct" type="float" optional="true" label="-t % occurance threshold before clipping (0.25)">
101 </param>
102 <param name="nmin" type="integer" optional="true" label="-m Minimum clip length, overrides scaled auto (1)">
103 </param>
104 <param name="pctdiff" type="integer" optional="true" label="-p Maximum adapter difference percentage (20)">
105 </param>
106
107 <param name="nmax" type="integer" optional="true" label="-L Maximum sequence length (none)">
108 </param>
109 <param name="nkeep" type="integer" optional="true" label="-l Minimum remaining sequence length (15)">
110 </param>
111 <param name="skewpct" type="float" optional="true" label="-k sKew percentage causing trimming (2)">
112 </param>
113 <param name="qthr" type="integer" optional="true" label="-q quality threshold causing trimming (7)"
114 help="remove end of-read with quality &lt; threshold">
115 </param>
116 <param name="qwin" type="integer" optional="true" label="-w mean quality threshold causing trimming (1)"
117 help="remove end of read with mean quality &lt; threshold">
118 </param>
119 <param name="pctns" type="float" optional="true" label="-x 'N' (Bad read) percentage causing trimming (10)">
120 </param>
121 <param name="rmns" type="boolean" truevalue="-R" falsevalue="" checked="false" label="-R Don't remove N's from the fronts/ends of reads"/>
122 <param name="ilv3" type="select" label="illumina PF filtering">
123 <option value=" ">Default</option>
124 <option value="-U">Disable illumina PF filtering</option>
125 <option value="-u">Enable illumina PF filtering</option>
126 </param>
127 </when>
128 </conditional>
129
130
131 <param name="phred" type="integer" optional="true" label="-P phred-scale (64)" help="Default is to determine automatically">
132 </param>
133
134 <param name="noclip" type="boolean" truevalue="-n" falsevalue="" checked="false" label="-n Don't clip, just output what would be done"/>
135
136 </inputs>
137 <outputs>
138 <data name="log" format="txt" label="${tool.name} on ${on_string}: log"/>
139 <data name="reads_out" format_source="reads" label="${tool.name} on ${on_string}: reads">
140 <filter>noclip == False</filter>
141 </data>
142 <data name="mates_out" format_source="mates" label="${tool.name} on ${on_string}: mates">
143 <filter>(noclip == False and mates != None)</filter>
144 </data>
145 </outputs>
146 <tests>
147 </tests>
148 <help>
149 **What it does**
150
151 fastq-mcf_ attempts to:
152
153 Detect and remove sequencing adapters and primers
154 Detect limited skewing at the ends of reads and clip
155 Detect poor quality at the ends of reads and clip
156 Detect N's, and remove from ends
157 Remove reads with CASAVA 'Y' flag (purity filtering)
158 Discard sequences that are too short after all of the above
159 Keep multiple mate-reads in sync while doing all of the above
160
161 .. _fastq-mcf: http://code.google.com/p/ea-utils/wiki/FastqMcf
162 -----
163
164 **Input**
165
166 Fasta file of adapter sequences, for example::
167
168 > Genomic_DNA_oligonucleotide_sequences_Adapters_F
169 GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG
170 > Genomic_DNA_oligonucleotide_sequences_Adapters_R
171 ACACTCTTTCCCTACACGACGCTCTTCCGATCT
172 > Genomic_DNA_Sequencing_Primer
173 ACACTCTTTCCCTACACGACGCTCTTCCGATCT
174
175
176
177 Reads or Left-hand mates, for example::
178
179 @1539:931/1
180 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
181 +1539:931/1
182 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
183
184 Right-hand mates, for example::
185
186 @1539:931/2
187 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
188 +1539:931/2
189 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
190
191 -----
192
193 **Output**
194
195 A log file
196
197 A trimmed fastq of the reads
198
199 A trimmed fastq of the mates
200
201
202
203 </help>
204 </tool>