Mercurial > repos > nml > spades_fasta_header_fixer
annotate spades_header_fixer.xml @ 1:4a80a8ffb288 draft
planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3051c6185128618cb9f137a10f45c248f6a6097f
author | nml |
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date | Fri, 02 Sep 2022 20:18:41 +0000 |
parents | f57f28bdd39b |
children | 2cc9e69419d2 |
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1
4a80a8ffb288
planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3051c6185128618cb9f137a10f45c248f6a6097f
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1 <tool id="spades_header_fixer" name="SPAdes fasta header fixer" version="1.1.2+galaxy0"> |
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f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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2 <description>Fixes Spades Fasta ids</description> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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3 <requirements> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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4 <requirement type="package" version="4.7.0">sed</requirement> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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5 </requirements> |
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4a80a8ffb288
planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3051c6185128618cb9f137a10f45c248f6a6097f
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6 <command >sed -r "s/>NODE(_[0-9]+)_(.*)|>contig/>${input.element_identifier}\1 \2/g" $input >$output</command> |
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f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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7 <inputs> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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8 <param name="input" type="data" format="fasta" label="Fix these fasta headers"/> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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9 </inputs> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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10 <outputs> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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11 <data name="output" format="fasta"/> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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12 </outputs> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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13 <tests> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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14 <test> |
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4a80a8ffb288
planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3051c6185128618cb9f137a10f45c248f6a6097f
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15 <param name="input" value="spades_before_1.fasta" /> |
4a80a8ffb288
planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3051c6185128618cb9f137a10f45c248f6a6097f
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16 <output name="output" file="spades_header_fixed_1.fasta" ftype="fasta"/> |
4a80a8ffb288
planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3051c6185128618cb9f137a10f45c248f6a6097f
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17 </test> |
4a80a8ffb288
planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3051c6185128618cb9f137a10f45c248f6a6097f
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18 <test> |
4a80a8ffb288
planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3051c6185128618cb9f137a10f45c248f6a6097f
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19 <param name="input" value="spades_before_2.fasta" /> |
4a80a8ffb288
planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3051c6185128618cb9f137a10f45c248f6a6097f
nml
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20 <output name="output" file="spades_header_fixed_2.fasta" ftype="fasta"/> |
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f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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21 </test> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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22 </tests> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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23 |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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24 <help><![CDATA[ |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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25 SPAdes fasta header fixer |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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26 ======= |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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27 |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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28 The SPAdes header fixer tool replaces the default value of NODE from SPAdes fasta header(s) to either a filename or a collection identifier. |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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29 ]]></help> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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30 |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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31 <citations> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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32 <citation type="bibtex">@ARTICLE{a1, |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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33 title = {SPAdes fasta header fixer}, |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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34 author = {Philip Mabon}, |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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35 url = {https://github.com/phac-nml/galaxy_tools} |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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36 } |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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37 }</citation> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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38 </citations> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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39 </tool> |