diff ipcress.xml @ 5:b321e0517be3 draft

Uploaded

--- /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>