Mercurial > repos > john-mccallum > ssr_marker_design
diff MISA/misa2gff.xml @ 2:16b5aa275b42 default tip
Uploaded minor revision to gff converter
| author | john-mccallum |
|---|---|
| date | Wed, 23 Nov 2011 19:15:31 -0500 |
| parents | e9f5d1afba70 |
| children |
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--- a/MISA/misa2gff.xml Tue Nov 22 14:46:23 2011 -0500 +++ b/MISA/misa2gff.xml Wed Nov 23 19:15:31 2011 -0500 @@ -1,48 +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> - +<tool id="misa2gff_1" name="MISA to GFF3"> + <description>convert MISA to gvf/gff3</description> + <command >cat $inputFile | awk '!/ID\W/ {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> +