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annotate mlst_list.xml @ 2:11e1af1f7f35 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 305238bd9771875830e8f4e961d16f0d7253e724
author iuc
date Mon, 12 Feb 2018 05:18:03 -0500
parents 681a5aa83361
children 022dc4bbc27e
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11e1af1f7f35 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 305238bd9771875830e8f4e961d16f0d7253e724
iuc
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1 <tool id="mlst_list" name="MLST List" version="2.10">
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2 <requirements>
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3 <requirement type="package" version="2.10">mlst</requirement>
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4 </requirements>
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6 <version_command>mlst --version</version_command>
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8 <command detect_errors="exit_code"><![CDATA[
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9 mlst $list_type > "$report"
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10 ]]></command>
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12 <inputs>
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13 <param name="list_type" type="boolean" label="Output allele information" truevalue="--longlist" falsevalue="--list"
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14 help="Selecting 'Yes' will provide the alleles for all MLST schemes" optional="false" />
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15 </inputs>
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17 <outputs>
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18 <data format="txt" name="report" label="${tool.name} - list of schemes"/>
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19 </outputs>
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21 <tests>
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22 <!-- Test the longlist option -->
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23 <test>
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24 <param name="list_type" value="true" />
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25 <output name="report" ftype="txt" >
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26 <assert_contents>
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27 <has_text text="saureus" />
681a5aa83361 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 47ad236b09eaf7541fbd7dd5b95e970800d545a5
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28 </assert_contents>
681a5aa83361 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 47ad236b09eaf7541fbd7dd5b95e970800d545a5
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29 </output>
0
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30 </test>
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32 <!-- Test the list option -->
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33 <test>
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34 <param name="list_type" value="false" />
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35 <output name="report" ftype="txt" >
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36 <assert_contents>
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37 <has_text text="saureus" />
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38 </assert_contents>
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39 </output>
0
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40 </test>
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41 </tests>
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43 <help><![CDATA[
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44 **What it does**
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46 MLST List will list all the scheme names used by MLST. Selecting the long list option will also provide the alleles for all MLST schemes.
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47
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48 ]]></help>
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49
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50 <citations>
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51 <citation type="bibtex">
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52 @UNPUBLISHED{Seemann2016,
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53 author = "Seemann T",
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54 title = "ABRicate: mass screening of contigs for antiobiotic resistance genes",
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55 year = "2016",
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56 note = "https://github.com/tseemann/abricate"}
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57 </citation>
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58 </citations>
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59 </tool>