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comparison design_primers.xml @ 5:b321e0517be3 draft

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author ben-warren
date Thu, 22 May 2014 20:30:19 -0400
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4:be070a68521e 5:b321e0517be3
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="Genetic_Marker_Design_2" name="Design primers to features"> 2 <tool id="Genetic_Marker_Design_2" name="Design primers to features">
3 <description>Design PCR Primers to Features</description> 3 <description>Design PCR Primers to Features</description>
4 <command interpreter="python">design_primers.py $inputfastaFile $inputSNPfile $inputTargetfile $min_size $max_size > $primer_outputfile </command> 4 <command interpreter="python -W ignore">
5 #if 'Yes' in $uMelt.value
6 design_primers.py -i $inputfastaFile -g $inputSNPfile -T $inputTargetfile -p $min_size -P $max_size -u > $primer_outputfile
7 #else
8 design_primers.py -i $inputfastaFile -g $inputSNPfile -T $inputTargetfile -p $min_size -P $max_size > $primer_outputfile
9 #end if
10 </command>
11
5 <inputs> 12 <inputs>
6 <param format="fasta" name="inputfastaFile" type="data" label="Multifasta Source file" /> 13 <param format="fasta" name="inputfastaFile" type="data" label="Multifasta Source file" />
7 <param format="gff3" name="inputSNPfile" type="data" label="annotation file(Gff3)" /> 14 <param format="gff3" name="inputSNPfile" type="data" label="annotation file(Gff3)" />
8 <param format="txt" name="inputTargetfile" type="data" optional="false" label="Target file" help="IN FORMAT Sequence id:source:type:start e.g. 1174806:gsMapper:SNP:292" ></param> 15 <param format="txt" name="inputTargetfile" type="data" optional="false" label="Target file" help="IN FORMAT Sequence id:source:type:start e.g. 1174806:gsMapper:SNP:292" ></param>
9 <param name="min_size" size="20" type="text" value="75" label="Minimum Product Size Range" /> 16 <param name="min_size" size="20" type="text" value="75" label="Minimum Product Size Range" />
10 <param name="max_size" size="20" type="text" value="100" label="Maximum Product Size Range" /> 17 <param name="max_size" size="20" type="text" value="100" label="Maximum Product Size Range" />
11 </inputs> 18 <param name="uMelt" type="select" label="uMelt prediction for HRM">
19 <option value="No" selected= "true">No</option>
20 <option value="Yes">Yes</option>
21 </param>
22 </inputs>
12 <outputs> 23 <outputs>
13 <data format="tabular" name="primer_outputfile" /> 24 <data format="tabular" name="primer_outputfile" />
14 </outputs> 25 </outputs>
15 <help> 26 <help>
16 .. class:: infomark 27 .. class:: infomark
17 28
18 **TIP** 29 **TIP**
19 30
20 This tool designs primer pairs to flank features 31 This tool designs primer pairs to flank features
32 Optionally it can predict reference and variant Tm using the uMelt web service provided by University of Utah
21 33
22 It takes 34 It takes
23 35
24 * an input reference sequence file 36 * an input reference sequence file
25 * a gff3 file containing feature information 37 * a gff3 file containing feature information