Mercurial > repos > john-mccallum > pcr_markers
diff ipcress.xml @ 5:b321e0517be3 draft
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author | ben-warren |
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date | Thu, 22 May 2014 20:30:19 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ipcress.xml Thu May 22 20:30:19 2014 -0400 @@ -0,0 +1,56 @@ +<?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>