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comparison ipcress.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"?>
2 <tool id="ipcress" name="In-Silico PCR Experiment Simulation System">
3 <description>In-Silico PCR Experiment Simulation System</description>
4 <version_command>ipcress -v</version_command>
5 <command>
6 awk -v min=$min_length -v max=$max_length '{print $1,$2,$3, min, max}' $input_primers | ipcress -i /dev/stdin -s $input_seqs -m $mismatch $products_as_fasta $pretty -S $seed_length > $pcr_products
7 </command>
8 <inputs>
9 <param format="txt" name="input_primers" type="data" label="PCR Experiment Data" />
10 <param format="fasta" name="input_seqs" type="data" label="Sequences (Fasta)" />
11 <param name="mismatch" size="10" type="integer" value="0" label="Mismatches allowed per primer" />
12 <param name="min_length" size="10" type="integer" value="50" label="Minimum PCR product length" />
13 <param name="max_length" size="10" type="integer" value="100" label="Maximum PCR product length" />
14 <param name="products_as_fasta" type="boolean" truevalue="-P" falsevalue="" label="Display PCR products as a FASTA format sequence" />
15 <param name="pretty" type="boolean" truevalue="-p 1" falsevalue="-p 0" checked="true" label="Display Result in pretty format" />
16 <param name="seed_length" size="10" type="integer" value="12" label="Seed length: 0 => Use Full Primer Length" />
17 </inputs>
18 <outputs>
19 <data format="txt" name="pcr_products" />
20 </outputs>
21 <stdio>
22 <exit_code range="1:" level="fatal" description="Fatal Error" />
23 </stdio>
24 <tests>
25 <test>
26 <param name="input_primers" value="ipcress_test_input.txt" ftype="txt" />
27 <param name="input_seqs" value="targets.fasta" ftype="fasta" />
28 <output name="pcr_products" file="ipcress.out" />
29 </test>
30 </tests>
31 <help>
32 ipcress is the In-silico PCR Experiment Simulation System.
33
34 This is a tool for simulation of PCR experiments. You supply a file containing primers and a set of sequences, and it predicts PCR products.
35
36 INPUT FORMAT
37
38 The input for ipcress is a simple white-space delimited file describing
39 one experiment per line. Each line contains the following 5 fields:
40
41 id An identifier for this experiment
42 primer_A Sequence for the first primer
43 primer_B Sequence for the second primer
44 min_product_len Minimum product length to report
45 max_product_len Maximum product length to report
46
47 Here is an example line in this format:
48
49 ID0001 CATGCATGCATGC CGATGCANGCATGCT 900 1100
50
51 MANUAL
52
53 https://www.ebi.ac.uk/~guy/exonerate/ipcress.man.html
54
55 </help>
56 </tool>