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annotate blast_unmatched.xml @ 3:fffdb903f2d1 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 1db05fc1c4849528c99b149d482eb34d3a80f22e
author artbio
date Sun, 15 Oct 2017 19:30:10 -0400
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fffdb903f2d1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 1db05fc1c4849528c99b149d482eb34d3a80f22e
artbio
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1 <tool id="blast_unmatched" name="Blast Unmatched" version="0.5.0">
0
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>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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4 </requirements>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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5 <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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6 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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7 --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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8 --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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9 --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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10 ]]></command>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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11 <inputs>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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12 <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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13 <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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14 </inputs>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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15 <outputs>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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16 <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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17 </outputs>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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18 <tests>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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19 <test>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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20 <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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21 <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
artbio
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22 <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
artbio
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23 </test>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
artbio
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24 </tests>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
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25 <help><![CDATA[
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
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26 **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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27
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
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28 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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29
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
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30 .. _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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31
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
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32 ]]></help>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
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33 <citations>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
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34 </citations>
f3b63b59a1ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_unmatched commit 5bd801feb838592fbb1f6dd68b5f1a480042da40
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35 </tool>