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author oscar_b
date Wed, 14 Nov 2018 14:15:24 -0500
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1 <tool id="blosum" name="Blosum" version="0.5.0">
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2 <description>Scores for peptide alignment by sequence</description>
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3 <requirements>
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4 <requirement type="package" version="8">openjdk</requirement>
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5 </requirements>
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6 <command detect_errors="aggressive"><![CDATA[
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7 java -Djava.awt.headless=true -jar '$__tool_directory__/Blosum.jar' '$input'
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8 ]]></command>
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9 <inputs>
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10 <param name="input" type="data" format="tabular" label="Peptide Sequences"/>
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11 </inputs>
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12 <outputs>
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13 <data name="output" format="tabular" from_work_dir="BlosumOutput.csv" label="peptides with scores ${on_string}"/>
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14 </outputs>
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15 <tests>
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16 <test>
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17 <param name="input" ftype="tabular" value="input.csv"/>
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18 <output name="output">
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19 <assert_contents>
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20 <has_text text="33"/>
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21 </assert_contents>
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22 </output>
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23 </test>
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24 </tests>
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25 <help><![CDATA[
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26 This program calculates a score of similitude between peptide sequences as referenced to a master peptide sequence of interest
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27 ]]></help>
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28 <citations>
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29 <citation type="doi">10.1021/ja507164a</citation>
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30 </citations>
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31 </tool>
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