Mercurial > repos > dfornika > chewbbaca_prepexternalschema

annotate chewbbaca_prepexternalschema.xml @ 0:68e59c40b1ea draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
author dfornika
date Tue, 02 Jun 2020 00:23:09 +0000
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children eac851537d92
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68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
dfornika
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1 <tool id="chewbbaca_prepexternalschema" name="chewBBACA PrepExternalSchema" version="@TOOL_VERSION@+galaxy0">
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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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>
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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4 <requirement type="package" version="@TOOL_VERSION@">chewbbaca</requirement>
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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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[
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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7 mkdir input_files &&
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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8 #for $f in in str( $input_fasta ).split(','):
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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9 #set $filename = os.path.basename( str($f) ).replace(".dat", "")
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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10 ln -s ${f} input_files/${filename}.fasta
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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11 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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12 --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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13 -i 'input_files'
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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14 #if str( translation_table ) != "":
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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15 --tbl '${translation_table}'
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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16 #end if
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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17 --bsr '${bsr}'
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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18 --len '${len}'
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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19 -o schema
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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20 && tar -czf schema.tgz schema
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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21 ]]>
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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22 </command>
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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23 <inputs>
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="input_fasta" format="fasta" type="data" multiple="true" label="Schema files (fasta)" />
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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25 <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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26 <param name="min_len" type="integer" min="1" value="100" max="100000" optional="true" label="Minimum length" />
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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27 </inputs>
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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28 <outputs>
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="schema_zipped" format="zip" label="${tool.name}: on ${on_string}: Schema (zipped)" from_work_dir="schema.tgz"/>
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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30 <data name="invalid_alleles" format="txt" label="${tool.name}: on ${on_string}: Invalid Alleles" from_work_dir="schema_invalid_alleles.txt"/>
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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31 <data name="invalid_alleles" format="txt" label="${tool.name}: on ${on_string}: Invalid Genes" from_work_dir="schema_invalid_genes.txt"/>
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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32 <data name="summary_stats" format="txt" label="${tool.name}: on ${on_string}: Summary Stats" from_work_dir="schema_summary_stats.txt"/>
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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33 </outputs>
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
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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36 </tests>
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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37 <help><![CDATA[
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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38 ]]>
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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39 </help>
68e59c40b1ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
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40 <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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41 </tool>