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annotate embl2fa.xml @ 0:3c8c9911cf2a draft

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