annotate patman.xml @ 4:be070a68521e draft

Uploaded workflow from vcf file to CAPS
author john-mccallum
date Thu, 18 Oct 2012 19:47:07 -0400
parents a0689dc29b7f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
1 <?xml version="1.0"?>
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
2 <tool id="patman_1" name="search for patterns in DNA using PatMaN">
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
3 <description>search for approximate patterns in DNA libraries</description>
1
a0689dc29b7f Updated vcf to gff conversion tool
john-mccallum
parents: 0
diff changeset
4 <command>patman -a -e $edits -g $gaps -D $inputfastaFile -P $inputPatfile | sort | uniq > $patman_outputfile </command>
0
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
5 <inputs>
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
6 <param name="edits" type="integer" label="max N mismatches and or gaps" value="0" size="1" />
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
7 <param name="gaps" type="integer" label="max N gaps" value="0" size="1"/>
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
8 <param format="fasta" name="inputfastaFile" type="data" label="Multifasta target file" />
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
9 <param format="fasta" name="inputPatfile" type="data" label="Pattern fasta" />
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
10
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
11 </inputs>
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
12 <outputs>
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
13 <data format="tabular" name="patman_outputfile" />
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
14 </outputs>
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
15 <help>
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
16
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
17
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
18
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
19 This is a Galaxy wrapper for PatMaN: a DNA pattern matcher for short sequences
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
20
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
21 * Website https://bioinf.eva.mpg.de/patman/
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
22 * PubMed Citation_
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
23
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
24 *Inputs*
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
25
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
26 * Patterns in fasta format (create from tabular using tabular-to-fasta tool)
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
27 * Multifasta file of target sequences
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
28
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
29 *Output*
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
30
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
31 * 6 Column tabular interval data
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
32 * Columns Chrom, Pattern Name, Start, End, strand, N mismatches
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
33
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
34 ::
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
35
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
36 isotig05934 ACP818 368 389 + 0
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
37 isotig05934 ACP859 377 396 + 0
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
38 isotig06765 ACP822 448 468 + 0
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
39 isotig07088 ACP825 49 75 + 0
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
40 isotig07652 ACP830 199 218 + 0
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
41 isotig07652 ACP831 257 276 + 0
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
42 isotig10333 ACP837 474 497 + 0
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
43 isotig10393 ACP838 10 34 + 0
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
44
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
45
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
46
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
47 .. _Citation: http://www.ncbi.nlm.nih.gov/pubmed/18467344?dopt=Abstract
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
48
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
49
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
50 </help>
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
51 </tool>