view Scan_IUPAC_output_matches_per_seq.xml @ 1:764d562755bd draft

Fix README formatting.

<?xml version="1.0" encoding="utf-8"?>
<tool id="fasta_scan_iupac_per_seq" name="IUPAC scan and output matches per seq" version="@VERSION@">
  <description>Counts the matches to a given IUPAC</description>
  <macros>
    <import>motif_tools_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command><![CDATA[
  perl $__tool_directory__/Scan_IUPAC_output_matches_per_seq.pl $iupac $fasta $output $strand
  ]]></command>
  <inputs>
    <param name="iupac" type="text" label="IUPAC string" value="e.g. WGATAR" help="Enter an IUPAC string." size="20"/>
    <param format="fasta" name="fasta" type="data" label="FASTA file" help="Select a FASTA file containing the sequences to be scanned."/>
    <param name="strand" type="select" label="Select sequence strands to scan" help="Scan either both strands or only the forward strand.">
      <option value="0">Scan both strands</option>
      <option value="1">Only scan forward strand</option>
    </param>
  </inputs>
  <outputs>
    <data format="tabular" name="output" />
  </outputs>
  <tests>
    <test>
      <param name="iupac" value="WGATAR" />
      <param name="fasta" value="phix.fa" />
      <param name="strand" value="0" />
      <output name="output" file="iupac_matches_per_seq.out" />
    </test>
  </tests>

  <help>
.. class:: infomark

**What it does**

This tool will find all matches to a DNA pattern in the input DNA sequence, represented by an IUPAC string. The matches are non-overlapping, so searching with 'TTTT' in 'TTTTTTTT' will find two hits to the IUPAC. The output is a table that gives the seqname and the number of matches to the IUPAC per sequence.  This version is useful if you want to get a count of IUPAC matches per sequence (e.g. a binding region) and paste the numbers back into a spreadsheet.

IUPAC = Nucleotide(s):

A = A
 
C = C

G = G

T = T

M = A/C

R = A/G

W = A/T

S = C/G

Y = C/T

K = G/T

V = A/C/G

H = A/C/T

D = A/G/T

B = C/G/T

N = A/C/G/T
 
----

.. class:: infomark

**Options**

'IUPAC string' - can be entered as upper- or lower-case as the tool will force them to become upper-case, but will only accept the IUPAC codes listed above.

'Select sequence strands to scan' - Only scanning the forward strand if the input sequence is useful if the IUPAC is a palindrome (e.g. CANNTG).

----

.. class:: infomark

**Credits**

This Galaxy tool has been developed within the Bioinformatics Core Facility at the University of Manchester. It runs the Scan_IUPAC_output_matches_per_seq.pl Perl script that was written by Ian Donaldson.

Please kindly acknowledge both this Galaxy tool and Scan_IUPAC_output_matches_per_seq.pl if you use it.
  </help>

</tool>