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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
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0:217aedbdd0d0 1:b61f1466ce8f
1 <tool id="fastq_mcf" name="FastqMcf" version="1.0"> 1 <tool id="fastq_mcf" name="FastqMcf" version="1.0">
2 <description>sequence quality filtering and clipping</description> 2 <description>sequence quality filtering and clipping</description>
3 <requirements> 3 <requirements>
4 <requirement type="binary">fastq-mcf</requirement> 4 <requirement type="package" version="1.1.2-484">ea-utils</requirement>
5 </requirements> 5 </requirements>
6 <version_string>fastq-mcf -V</version_string> 6 <version_string>fastq-mcf -V</version_string>
7 <command>fastq-mcf 7 <command>fastq-mcf
8 #if $trimming.choice == 'disable': 8 #if $trimming.choice == 'disable':
9 -0 9 -0
39 -x $trimming.pctns 39 -x $trimming.pctns
40 #end if 40 #end if
41 #if len($trimming.sampcnt.__str__) > 0 41 #if len($trimming.sampcnt.__str__) > 0
42 -s $trimming.sampcnt 42 -s $trimming.sampcnt
43 #end if 43 #end if
44 $trimming.ilv3 44 #if len($trimming.ilv3.__str__.strip()) > 0
45 -$trimming.ilv3
46 #end if
45 $trimming.rmns 47 $trimming.rmns
46 #end if 48 #end if
47 #if $noclip == True : 49 #if $noclip == True :
48 $noclip 50 $noclip
49 #else : 51 #else :
118 </param> 120 </param>
119 <param name="pctns" type="float" optional="true" label="-x 'N' (Bad read) percentage causing trimming (10)"> 121 <param name="pctns" type="float" optional="true" label="-x 'N' (Bad read) percentage causing trimming (10)">
120 </param> 122 </param>
121 <param name="rmns" type="boolean" truevalue="-R" falsevalue="" checked="false" label="-R Don't remove N's from the fronts/ends of reads"/> 123 <param name="rmns" type="boolean" truevalue="-R" falsevalue="" checked="false" label="-R Don't remove N's from the fronts/ends of reads"/>
122 <param name="ilv3" type="select" label="illumina PF filtering"> 124 <param name="ilv3" type="select" label="illumina PF filtering">
123 <option value=" ">Default</option> 125 <option value="">Default</option>
124 <option value="-U">Disable illumina PF filtering</option> 126 <option value="U">Disable illumina PF filtering</option>
125 <option value="-u">Enable illumina PF filtering</option> 127 <option value="u">Enable illumina PF filtering</option>
126 </param> 128 </param>
127 </when> 129 </when>
128 </conditional> 130 </conditional>
129 131
130 132
141 </data> 143 </data>
142 <data name="mates_out" format_source="mates" label="${tool.name} on ${on_string}: mates"> 144 <data name="mates_out" format_source="mates" label="${tool.name} on ${on_string}: mates">
143 <filter>(noclip == False and mates != None)</filter> 145 <filter>(noclip == False and mates != None)</filter>
144 </data> 146 </data>
145 </outputs> 147 </outputs>
148 <stdio>
149 <exit_code range="1:" level="fatal" description="Error" />
150 </stdio>
146 <tests> 151 <tests>
152 <test>
153 <param name="adpaters" ftype="fasta" value="adapters.fa" />
154 <param name="reads" ftype="fastqillumina" value="test_mcf_reads.fq" />
155 <param name="mates" ftype="fastqillumina" value="test_mcf_mates.fq" />
156 <param name="choice" value="user_set" />
157 <param name="nkeep" value="16" />
158 <param name="qthr" value="15" />
159 <param name="qwin" value="5" />
160 <param name="pctns" value="10" />
161 <param name="ilv3" value="u" />
162 <param name="phred" value="33" />
163 <output name="reads_out" file="testout_mcf_reads.fq" />
164 <output name="mates_out" file="testout_mcf_mates.fq" />
165 </test>
147 </tests> 166 </tests>
148 <help> 167 <help>
149 **What it does** 168 **What it does**
150 169
151 fastq-mcf_ attempts to: 170 fastq-mcf_ attempts to:
154 Detect limited skewing at the ends of reads and clip 173 Detect limited skewing at the ends of reads and clip
155 Detect poor quality at the ends of reads and clip 174 Detect poor quality at the ends of reads and clip
156 Detect N's, and remove from ends 175 Detect N's, and remove from ends
157 Remove reads with CASAVA 'Y' flag (purity filtering) 176 Remove reads with CASAVA 'Y' flag (purity filtering)
158 Discard sequences that are too short after all of the above 177 Discard sequences that are too short after all of the above
178
179
159 Keep multiple mate-reads in sync while doing all of the above 180 Keep multiple mate-reads in sync while doing all of the above
160 181
161 .. _fastq-mcf: http://code.google.com/p/ea-utils/wiki/FastqMcf 182 .. _fastq-mcf: http://code.google.com/p/ea-utils/wiki/FastqMcf
162 ----- 183 -----
163 184