Mercurial > repos > artbio > embl2fa
comparison embl2fa.xml @ 0:3c8c9911cf2a draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/embl2fa commit 6e5860cedc0ed0bc807ff64f752e62355c1b19d4
| author | artbio |
|---|---|
| date | Sun, 13 Nov 2022 00:23:23 +0000 |
| parents | |
| children | a0b6fec3b066 |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:3c8c9911cf2a |
|---|---|
| 1 <tool id="embl2fa" name="Convert embl flat file to fasta" version="0.1"> | |
| 2 <description></description> | |
| 3 <stdio> | |
| 4 <exit_code range="1:" level="fatal" description="Tool exception" /> | |
| 5 </stdio> | |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 7 grep -P "(^ID)|(^ +[GATCNgatcn ]+\d+)" "$input" > "$output" && | |
| 8 sed -i -E "s/^ID />/" "$output" && | |
| 9 sed -i -E "s/(>[^ ]+) .+/\1/g" "$output" && | |
| 10 sed -i -E "s/([GATCNgatcn]+) /\1/g" "$output" && | |
| 11 sed -i -E "s/^ +//g" "$output" && | |
| 12 sed -i -E "s/ +[0-9]+//g" "$output" | |
| 13 ]]></command> | |
| 14 <inputs> | |
| 15 <param format="txt" name="input" type="data" label="EMBL flat file" /> | |
| 16 </inputs> | |
| 17 <outputs> | |
| 18 <data name="output" format="fasta" label="fasta file" /> | |
| 19 </outputs> | |
| 20 <tests> | |
| 21 <test> | |
| 22 <param name="input" value="transposon_sequence_set_v9.5.embl.txt" ftype="txt" /> | |
| 23 <output name="output" file="transposon_sequence_set_v9.5.fa" ftype="fasta"/> | |
| 24 </test> | |
| 25 </tests> | |
| 26 <help> | |
| 27 | |
| 28 .. class:: infomark | |
| 29 | |
| 30 **What it does** | |
| 31 | |
| 32 Converts file in EMBL flat format to fasta file | |
| 33 </help> | |
| 34 </tool> | |
| 35 |