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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit ecebab288909d75a9f6e86d34a5c85e246678ab2
author iuc
date Wed, 15 Jun 2022 18:59:31 +0000
parents 7eb5e58d2263
children
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022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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1 <tool id="mlst_list" name="MLST List" version="@VERSION@">
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7eb5e58d2263 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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2 <description>Lists available schemes for the MLST tool</description>
7eb5e58d2263 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <xrefs>
7eb5e58d2263 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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4 <xref type="bio.tools">mlst</xref>
7eb5e58d2263 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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5 </xrefs>
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022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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6 <macros>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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7 <import>macros.xml</import>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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8 </macros>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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9 <expand macro="requirements" />
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
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10 <expand macro="version_command" />
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12 <command detect_errors="exit_code"><![CDATA[
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13 mlst $list_type > '$report'
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14 ]]></command>
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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16 <inputs>
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17 <param name="list_type" type="boolean" label="Output allele information" truevalue="--longlist" falsevalue="--list"
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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18 help="Selecting 'Yes' will provide the alleles for all MLST schemes" optional="false" />
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19 </inputs>
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21 <outputs>
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22 <data format="txt" name="report" label="${tool.name} - list of schemes"/>
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23 </outputs>
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25 <tests>
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26 <!-- Test the longlist option -->
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27 <test>
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
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28 <param name="list_type" value="true" />
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29 <output name="report" ftype="txt" >
681a5aa83361 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 47ad236b09eaf7541fbd7dd5b95e970800d545a5
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30 <assert_contents>
681a5aa83361 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 47ad236b09eaf7541fbd7dd5b95e970800d545a5
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31 <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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32 </assert_contents>
681a5aa83361 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 47ad236b09eaf7541fbd7dd5b95e970800d545a5
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33 </output>
0
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34 </test>
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36 <!-- Test the list option -->
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37 <test>
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38 <param name="list_type" value="false" />
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39 <output name="report" ftype="txt" >
681a5aa83361 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 47ad236b09eaf7541fbd7dd5b95e970800d545a5
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40 <assert_contents>
681a5aa83361 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 47ad236b09eaf7541fbd7dd5b95e970800d545a5
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41 <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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42 </assert_contents>
681a5aa83361 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 47ad236b09eaf7541fbd7dd5b95e970800d545a5
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43 </output>
0
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44 </test>
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45 </tests>
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47 <help><![CDATA[
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48 **What it does**
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50 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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52 ]]></help>
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54 <expand macro="citations" />
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55 </tool>