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annotate linelisting.xml @ 2:141cbefca027 draft default tip

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planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 6f09c69c51ec3d6bd7487f55384b97155355c456
author public-health-bioinformatics
date Mon, 04 Feb 2019 18:35:20 -0500
parents 8a4ee4be0b7e
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bda72dec1f55 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 856d0b7ab7dc801c168fcdf45cfd2e31f062a37e-dirty
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1 <tool id="linelisting" name="Line List" version="0.0.1">
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2 <requirements>
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3 <requirement type="package" version="1.70">biopython</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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8a4ee4be0b7e planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit e6d31e4b3666b5e1d322e22f44526f23c66692fb
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6 python $__tool_directory__/linelisting.py
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bda72dec1f55 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 856d0b7ab7dc801c168fcdf45cfd2e31f062a37e-dirty
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7 '$input_fasta'
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8 '$ref_fasta'
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9 '$index_array_csv'
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10 '$clade_def_csv'
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11 '$output_file'
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12 ]]></command>
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13 <inputs>
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14 <param name="input_fasta" format="fasta" type="data" label="Sample Sequences fasta."/>
bda72dec1f55 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 856d0b7ab7dc801c168fcdf45cfd2e31f062a37e-dirty
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15 <param name="ref_fasta" format="fasta" type="data" label="Reference Sequence fasta."/>
bda72dec1f55 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 856d0b7ab7dc801c168fcdf45cfd2e31f062a37e-dirty
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16 <param name="index_array_csv" format="csv" type="data" label="Antigenic Site Index Array File."/>
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17 <param name="clade_def_csv" format="csv" type="data" label="Clade Definition File."/>
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18 </inputs>
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19 <outputs>
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20 <data name="output_file" format="csv"/>
bda72dec1f55 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 856d0b7ab7dc801c168fcdf45cfd2e31f062a37e-dirty
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21 </outputs>
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22 <tests>
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23 <test>
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141cbefca027 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 6f09c69c51ec3d6bd7487f55384b97155355c456
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24 <param name="input_fasta" value="fluA_H3_clade_assigned_antigenic_sites_extracted.fasta"/>
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25 <param name="ref_fasta" value="MAP_3C.2a_A_Hong_Kong_4801_2014_X-263B_EGG.fasta" />
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26 <param name="index_array_csv" value="FluA_H3_antigenic_aa_indices.csv" />
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27 <param name="clade_def_csv" value="Flu_Clade_Definitions_H3_20171121.csv" />
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28 <output name="output_file" value="test_output.csv"/>
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29 </test>
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30 </tests>
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31 <help><![CDATA[
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32 ]]></help>
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33 <citations>
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34 </citations>
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35 </tool>