Mercurial > repos > iuc > chewbbaca_nsstats

annotate NSStats.xml @ 0:97a24534a0c0 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
author iuc
date Wed, 25 Sep 2024 14:12:51 +0000
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97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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1 <tool id="chewbbaca_nsstats" name="chewBBACA NSStats" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Retrieve basic information about the species and schemas in Chewie-NS</description>
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3 <macros>
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4 <import>macros.xml</import>
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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5 </macros>
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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6 <expand macro="requirements" />
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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7 <command detect_errors="exit_code"><![CDATA[
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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8 chewBBACA.py NSStats
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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9 -m $mode
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10 #if $species_id != ""
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11 --sp $species_id
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12 #end if
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13 #if $schema_id != ""
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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14 --sc $schema_id
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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15 #end if
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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16 > 'NSStats.txt'
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17 ]]></command>
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18 <inputs>
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19 <param argument="--mode" type="select" label="Mode" optional="false">
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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20 <option value="species">species</option>
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21 <option value="schemas">schemas</option>
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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22 </param>
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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23 <param argument="--species-id" type="select" label="Species ID" value="" optional="true">
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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24 <expand macro="species_id"/>
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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25 </param>
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26 <!-- Currently,the schema id can only be set to 1. Maybe in the next versions other values possible -->
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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27 <param argument="--schema-id" type="integer" min="1" value="" label="Schema ID" optional="true"/>
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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28 </inputs>
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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29 <outputs>
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30 <data format="txt" name="NSStats" from_work_dir="NSStats.txt" label="${tool.name}"/>
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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31 </outputs>
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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32 <tests>
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33 <test expect_exit_code="0">
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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34 <param name="mode" value="species" />
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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35 <output name="NSStats">
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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36 <assert_contents>
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37 <has_text_matching expression="Streptococcus pyogenes\s+1\s+1\s+3044\s+398511"/>
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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38 <has_text_matching expression="Clostridium neonatale\s+16\s+1\s+2350\s+13115"/>
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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39 </assert_contents>
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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40 </output>
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41 </test>
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42 </tests>
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43 <help>
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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44 chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
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45
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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46 The NSStats module enables the retrieval of information from the Chewie-NS server. Its main objective is to provide information about the list of species and schemas in Chewie-NS, so that users can quickly identify a schema of interest and download it.
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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47
97a24534a0c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
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48 </help>
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49 <expand macro="citations" />
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50 </tool>