Mercurial > repos > john-mccallum > pcr_markers
comparison design_primers.xml @ 5:b321e0517be3 draft
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author | ben-warren |
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date | Thu, 22 May 2014 20:30:19 -0400 |
parents | a0689dc29b7f |
children | f201e8c6e004 |
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4:be070a68521e | 5:b321e0517be3 |
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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 |