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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched commit 4a20557bdd1306b701fd5bc61f9d0aceb24da0d5
author artbio
date Wed, 11 Oct 2023 11:12:34 +0000
parents caa54ff096c8
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d0c2a559fe1b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched commit 4a20557bdd1306b701fd5bc61f9d0aceb24da0d5
artbio
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1 <tool id="blast_unmatched" name="Blast Unmatched" version="1.0.1">
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f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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2 <description>get query sequences that didn't get a match during a blast</description>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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3 <requirements>
4
caa54ff096c8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 3dcf4e7314dd6a4fefcd721ac58c8130dd1da2a1"
artbio
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4 <requirement type="package" version="3.7.6">python</requirement>
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f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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5 </requirements>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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6 <command detect_errors="exit_code"><![CDATA[
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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7 python '$__tool_directory__'/blast_unmatched.py
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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8 --fasta $fasta_file
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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9 --blast $blast_file
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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10 --output $output_file
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
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11 ]]></command>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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12 <inputs>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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13 <param type="data" name="fasta_file" format="fasta"/>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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14 <param type="data" name="blast_file" format="tabular"/>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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15 </inputs>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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16 <outputs>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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17 <data name="output_file" format="fasta" label="Unmatched queries from blast: ${blast_file.name}"/>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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18 </outputs>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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19 <tests>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
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20 <test>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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21 <param name="blast_file" value="test_blast.tab"/>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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22 <param name="fasta_file" value="test_query.fa"/>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
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23 <output name="output_file" ftype="fasta" file="test_output.fa"/>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
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24 </test>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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25 </tests>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
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26 <help><![CDATA[
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
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27 **What it does**
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
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28
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
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29 This tool takes a `blast`_ output in tabular format(with the query id in 1rst column) and the fasta file used as query. It then return the query sequences that remained unmatched during the blast.
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
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30
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
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31 .. _blast: https://blast.ncbi.nlm.nih.gov/Blast.cgi
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
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32
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
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33 ]]></help>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
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34 <citations>
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d0c2a559fe1b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched commit 4a20557bdd1306b701fd5bc61f9d0aceb24da0d5
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35 <citation type="doi">10.1186/s13742-015-0080-7</citation>
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f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
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36 </citations>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
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37 </tool>