Mercurial > repos > oscar_b > blosum
comparison Blosum.xml @ 1:164c74b7d943 draft
planemo upload commit 524a261eaa7126369f1b292aa44ce541f720fd83
| author | oscar_b |
|---|---|
| date | Wed, 14 Nov 2018 13:34:09 -0500 |
| parents | 4438273d5b7f |
| children | e25074cb4dbb |
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| 0:4438273d5b7f | 1:164c74b7d943 |
|---|---|
| 1 <tool id="blosum" name="Blosum" version="0.5.0"> | 1 <tool id="blosum" name="Blosum" version="0.5.0"> |
| 2 <description>Scores for peptide alignment by sequence</description> | 2 <description>Scores for peptide alignment by sequence</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package">openjdk</requirement> | 4 <requirement type="package" version="8">openjdk</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <command detect_errors="aggressive"><![CDATA[ | 6 <command detect_errors="aggressive"><![CDATA[ |
| 7 java -Djava.awt.headless=true -jar '$__tool_directory__/Blosum.jar' | 7 java -Djava.awt.headless=true -jar '$__tool_directory__/Blosum.jar' |
| 8 ]]></command> | 8 ]]></command> |
| 9 <inputs> | 9 <inputs> |
| 10 <param format="csv" name="input" type="data" label="Peptide Sequences"/> | 10 <param name="input" type="data" format="tabular" label="Peptide Sequences"/> |
| 11 </inputs> | 11 </inputs> |
| 12 <outputs> | 12 <outputs> |
| 13 <data format="csv" name="output" from_work_dir="output.csv" label="peptides with scores ${on_string}"/> | 13 <data name="output" format="tabular" from_work_dir="output.csv" label="peptides with scores ${on_string}"/> |
| 14 </outputs> | 14 </outputs> |
| 15 <tests> | 15 <tests> |
| 16 <test> | 16 <test> |
| 17 <param name="input" ftype="tabular" value="input.csv"/> | |
| 18 <output name="output"> | |
| 19 <assert_contents> | |
| 20 <has_text text="33"/> | |
| 21 </assert_contents> | |
| 22 </output> | |
| 17 </test> | 23 </test> |
| 18 </tests> | 24 </tests> |
| 19 | |
| 20 | |
| 21 <help><![CDATA[ | 25 <help><![CDATA[ |
| 22 This program calculates a score of similitude between peptide sequences as referenced to a master peptide sequence of interest | 26 This program calculates a score of similitude between peptide sequences as referenced to a master peptide sequence of interest |
| 23 ]]></help> | 27 ]]></help> |
| 24 <citations> | 28 <citations> |
| 25 <citation type="doi">10.1021/ja507164a</citation> | 29 <citation type="doi">10.1021/ja507164a</citation> |