Mercurial > repos > john-mccallum > ssr_marker_design
changeset 1:e9f5d1afba70
Uploaded misa2gff tool
| author | john-mccallum |
|---|---|
| date | Tue, 22 Nov 2011 14:46:23 -0500 |
| parents | 3006582bfc76 |
| children | 16b5aa275b42 |
| files | MISA/misa2gff.xml |
| diffstat | 1 files changed, 48 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MISA/misa2gff.xml Tue Nov 22 14:46:23 2011 -0500 @@ -0,0 +1,48 @@ +<tool id="misa2gff_1" name="MISA to GFF3"> + <description>convert MISA to gvf/gff3</description> + <command >cat $inputFile | awk '(NR > 1) {OFS="\t";print $1,"MISA","microsatellite",$6,$7,".",".",".","ID="$1":MISA:microsatellite:"$6";SSR="$4,";Type="$3}' > $outputfile</command> + <inputs> + <param format="tabular" name="inputFile" type="data" label="Input MISA File" help="MISA file from MISA.pl" /> + </inputs> + <outputs> +<data format="gff3" name="outputfile" /> + + </outputs> + +<help> + +.. class:: infomark + +**TIP** + +This tool parses MISA columnar output to valid GFF3 format + +------------------- + +**Example** + +*input* + +:: + + ID SSR nr. SSR type SSR size start end + FW9DLND01C1Y2S 1 p2 (AC)11 22 89 110 + FW9DLND01CSIIJ 1 p2 (AC)7 14 226 239 + FW9DLND01DOGBK 1 p1 (A)12 12 162 173 + FW9DLND01B7MCF 1 p2 (AT)7 14 22 35 + FW9DLND01DHCGH 1 p2 (AT)7 14 108 121 + +*output* + +:: + + FW9DLND01C1Y2S MISA microsatellite 89 110 . . . ID=FW9DLND01C1Y2S:MISA:microsatellite:89;SSR=(AC)11 ;Type=p2 + FW9DLND01CSIIJ MISA microsatellite 226 239 . . . ID=FW9DLND01CSIIJ:MISA:microsatellite:226;SSR=(AC)7 ;Type=p2 + FW9DLND01DOGBK MISA microsatellite 162 173 . . . ID=FW9DLND01DOGBK:MISA:microsatellite:162;SSR=(A)12 ;Type=p1 + FW9DLND01B7MCF MISA microsatellite 22 35 . . . ID=FW9DLND01B7MCF:MISA:microsatellite:22;SSR=(AT)7 ;Type=p2 + FW9DLND01DHCGH MISA microsatellite 108 121 . . . ID=FW9DLND01DHCGH:MISA:microsatellite:108;SSR=(AT)7 ;Type=p2 + + +</help> +</tool> +