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<?xml version="1.0"?>
<tool id="ipcress" name="In-Silico PCR Experiment Simulation System">
        <description>In-Silico PCR Experiment Simulation System</description>
        <version_command>ipcress -v</version_command>
        <command>
                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
        </command>
        <inputs>
                <param format="txt" name="input_primers" type="data" label="PCR Experiment Data" />
                <param format="fasta" name="input_seqs" type="data" label="Sequences (Fasta)" />
                <param name="mismatch" size="10" type="integer" value="0" label="Mismatches allowed per primer" />
                <param name="min_length" size="10" type="integer" value="50" label="Minimum PCR product length" />
                <param name="max_length" size="10" type="integer" value="100" label="Maximum PCR product length" />
                <param name="products_as_fasta" type="boolean" truevalue="-P" falsevalue="" label="Display PCR products as a FASTA format sequence" />
                <param name="pretty" type="boolean" truevalue="-p 1" falsevalue="-p 0" checked="true" label="Display Result in pretty format" />
                <param name="seed_length" size="10" type="integer" value="12" label="Seed length: 0 => Use Full Primer Length" />
        </inputs>
        <outputs>
                <data format="txt" name="pcr_products" />
        </outputs>
        <stdio>
                <exit_code range="1:" level="fatal" description="Fatal Error" />
        </stdio>
        <tests>
        <test>
                <param name="input_primers" value="ipcress_test_input.txt" ftype="txt" />
                <param name="input_seqs" value="targets.fasta" ftype="fasta" />
                <output name="pcr_products" file="ipcress.out" />
        </test>
        </tests>
        <help>
ipcress is the In-silico PCR Experiment Simulation System.

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.

INPUT FORMAT

The input for ipcress is a simple white-space delimited file describing
one experiment per line.  Each line contains the following 5 fields:

id                An identifier for this experiment
primer_A          Sequence for the first primer
primer_B          Sequence for the second primer
min_product_len   Minimum product length to report
max_product_len   Maximum product length to report

Here is an example line in this format:

ID0001 CATGCATGCATGC CGATGCANGCATGCT 900 1100

MANUAL

https://www.ebi.ac.uk/~guy/exonerate/ipcress.man.html

        </help>
</tool>