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1 <?xml version="1.0"?>
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2 <tool id="ipcress" name="In-Silico PCR Experiment Simulation System">
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3 <description>In-Silico PCR Experiment Simulation System</description>
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4 <version_command>ipcress -v</version_command>
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5 <command>
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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
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7 </command>
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8 <inputs>
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9 <param format="txt" name="input_primers" type="data" label="PCR Experiment Data" />
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10 <param format="fasta" name="input_seqs" type="data" label="Sequences (Fasta)" />
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11 <param name="mismatch" size="10" type="integer" value="0" label="Mismatches allowed per primer" />
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12 <param name="min_length" size="10" type="integer" value="50" label="Minimum PCR product length" />
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13 <param name="max_length" size="10" type="integer" value="100" label="Maximum PCR product length" />
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14 <param name="products_as_fasta" type="boolean" truevalue="-P" falsevalue="" label="Display PCR products as a FASTA format sequence" />
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15 <param name="pretty" type="boolean" truevalue="-p 1" falsevalue="-p 0" checked="true" label="Display Result in pretty format" />
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16 <param name="seed_length" size="10" type="integer" value="12" label="Seed length: 0 => Use Full Primer Length" />
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17 </inputs>
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18 <outputs>
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19 <data format="txt" name="pcr_products" />
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20 </outputs>
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21 <stdio>
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22 <exit_code range="1:" level="fatal" description="Fatal Error" />
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23 </stdio>
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24 <tests>
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25 <test>
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26 <param name="input_primers" value="ipcress_test_input.txt" ftype="txt" />
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27 <param name="input_seqs" value="targets.fasta" ftype="fasta" />
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28 <output name="pcr_products" file="ipcress.out" />
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29 </test>
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30 </tests>
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31 <help>
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32 ipcress is the In-silico PCR Experiment Simulation System.
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33
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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.
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35
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36 INPUT FORMAT
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37
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38 The input for ipcress is a simple white-space delimited file describing
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39 one experiment per line. Each line contains the following 5 fields:
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40
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41 id An identifier for this experiment
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42 primer_A Sequence for the first primer
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43 primer_B Sequence for the second primer
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44 min_product_len Minimum product length to report
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45 max_product_len Maximum product length to report
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46
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47 Here is an example line in this format:
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48
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49 ID0001 CATGCATGCATGC CGATGCANGCATGCT 900 1100
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50
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51 MANUAL
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52
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53 https://www.ebi.ac.uk/~guy/exonerate/ipcress.man.html
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54
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55 </help>
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56 </tool>
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