Mercurial > repos > nml > spades_fasta_header_fixer
annotate spades_header_fixer.xml @ 0:f57f28bdd39b draft
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
author | nml |
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date | Thu, 19 Dec 2019 10:07:39 -0500 |
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children | 4a80a8ffb288 |
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0
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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1 <tool id="spades_header_fixer" name="SPAdes fasta header fixer" version="1.1.1"> |
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> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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6 <command >sed -r "s/>NODE(_[0-9]+)_(.*)/>${input.element_identifier}\1 \2/g" $input >$output</command> |
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> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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15 <param name="input" value="spades_before.fasta" /> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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16 <output name="output" file="spades_header_fixed.fasta" ftype="fasta"/> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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17 </test> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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18 </tests> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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19 |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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20 <help><![CDATA[ |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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21 SPAdes fasta header fixer |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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22 ======= |
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"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 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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25 ]]></help> |
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"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 <citations> |
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"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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28 <citation type="bibtex">@ARTICLE{a1, |
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"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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29 title = {SPAdes fasta header fixer}, |
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"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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30 author = {Philip Mabon}, |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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31 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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32 } |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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33 }</citation> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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34 </citations> |
f57f28bdd39b
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
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35 </tool> |