Mercurial > repos > dfornika > chewbbaca_prepexternalschema

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 071e014d347109e5c18cc50595498d3d43ef0323-dirty"
author dfornika
date Wed, 03 Jun 2020 00:57:38 +0000
parents 0f665cf63c02
children
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eac851537d92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 071e014d347109e5c18cc50595498d3d43ef0323-dirty"
dfornika
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1 <tool id="chewbbaca_prepexternalschema" name="chewBBACA PrepExternalSchema" version="2.1.0+galaxy0">
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2 <description>Adapt an external schema to be used with chewBBACA.</description>
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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3 <requirements>
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eac851537d92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 071e014d347109e5c18cc50595498d3d43ef0323-dirty"
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4 <requirement type="package" version="2.1.0">chewbbaca</requirement>
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5 </requirements>
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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6 <command detect_errors="exit_code"><![CDATA[
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7 mkdir input_files &&
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8 #for $f in str( $input_fasta ).split(','):
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9 #set $filename = os.path.basename( str($f) ).replace(".dat", "")
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10 ln -s ${f} input_files/${filename}.fasta
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11 #end for
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12 chewBBACA.py PrepExternalSchema
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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13 --cpu \${GALAXY_SLOTS:-1}
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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14 -i 'input_files'
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15 --bsr '${bsr}'
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16 --len '${len}'
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17 -o schema
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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18 && tar -czf schema.tgz schema
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19 ]]>
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20 </command>
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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21 <inputs>
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22 <param name="input_fasta" format="fasta" type="data" multiple="true" label="Schema files (fasta)" />
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23 <param name="bsr" type="float" value="0.6" optional="true" label="BSR score" />
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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24 <param name="min_len" type="integer" min="1" value="100" max="100000" optional="true" label="Minimum length" />
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25 </inputs>
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26 <outputs>
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27 <data name="schema_zipped" format="zip" label="${tool.name}: on ${on_string}: Schema (zipped)" from_work_dir="schema.tgz"/>
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28 <data name="invalid_alleles" format="txt" label="${tool.name}: on ${on_string}: Invalid Alleles" from_work_dir="schema_invalid_alleles.txt"/>
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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29 <data name="invalid_alleles" format="txt" label="${tool.name}: on ${on_string}: Invalid Genes" from_work_dir="schema_invalid_genes.txt"/>
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30 <data name="summary_stats" format="txt" label="${tool.name}: on ${on_string}: Summary Stats" from_work_dir="schema_summary_stats.txt"/>
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31 </outputs>
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32 <tests>
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68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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34 </tests>
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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35 <help><![CDATA[
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36 ]]>
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37 </help>
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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38 <expand macro="citations"/>
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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39 </tool>