Mercurial > repos > pjbriggs > motif_tools
diff Scan_IUPAC_output_each_match.xml @ 0:b67ea47730d3 draft
Version 1.0.1.
author | pjbriggs |
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date | Wed, 21 Mar 2018 06:39:41 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Scan_IUPAC_output_each_match.xml Wed Mar 21 06:39:41 2018 -0400 @@ -0,0 +1,96 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="fasta_scan_iupac_each" name="IUPAC scan and output each match" version="@VERSION@"> + <description>Returns all matches to a given IUPAC in GFF format</description> + <macros> + <import>motif_tools_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command><![CDATA[ + perl $__tool_directory__/Scan_IUPAC_output_each_match.pl $iupac $fasta $output $label $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="label" type="text" label="Attribute in GFF output" value="IUPAC_or_name" help="The label will be included at the end (attibute) section of each GFF line. This could be the IUPAC string used or the name of the motif." size="20"/> + <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="gff" name="output" /> + </outputs> + <tests> + <test> + <param name="iupac" value="WGATAR" /> + <param name="fasta" value="phix.fa" /> + <param name="label" value="IUPAC_or_name" /> + <param name="strand" value="0" /> + <output name="output" file="iupac_each_match.gff" /> + </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 in GFF format and the last 'attribute' field can be specified using the 'Label' option. + +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. + +'Attribute in GFF output' - the last field of each GFF line 'attribute' can be specified using the 'Label' option, this should only include letters/numbers, but without spaces. + +'Select sequence strands to scan' - Only scanning the forward strand of 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_each_match.pl Perl script that was written by Ian Donaldson. + +Please kindly acknowledge both this Galaxy tool and Scan_IUPAC_output_each_match.pl if you use it. + </help> + +</tool> +