Mercurial > repos > iuc > mykrobe_genotype

annotate mykrobe_genotype.xml @ 1:84f769706f7a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
author iuc
date Tue, 02 Apr 2019 11:57:05 -0400
parents d783eb846f59
children 0f4a5de7878a
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84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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1 <tool id="mykrobe_genotype" name="mkyrobe genotype" version="0.6.1" >
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2 <description>Antibiotic resistance predictions</description>
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3 <macros>
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4 <import>macro.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 @select_inputs@
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11 mykrobe genotype
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12 '${name}'
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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13 '${probe_set}'
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1
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15 #if $filter:
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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16 --filters '${filter}'
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17 #end if
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18
1
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19 @shared_options@
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21 -q
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22 -t "\${GALAXY_SLOTS:-1}"
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24 -1
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25 #if $type == 'fastq':
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26 *.fastq
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27 #elif $type == 'bam':
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28 *.bam
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29 #else
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30 *.fasta
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31 #end if
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32 > '$json'
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33 ]]>
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34 </command>
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35 <inputs>
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36 <expand macro="inputs" />
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84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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37 <param argument="--probe_set" type="data" format="fasta" label="Probe Set"/>
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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38 <param argument="--filter" type="data" format="txt,fasta" label="Filter Genotypes" optional="True" help="Don't include filtered genotypes"/>
84f769706f7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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39 <expand macro="options"/>
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40 </inputs>
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41 <outputs>
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42 <data name="json" format="json" label="JSON prediction"/>
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="type" value="single"/>
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47 <param name="fastq_input1" value="reads.fastq"/>
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48 <param name="probe_set" value="tb-bradley-probe-set-feb-09-2017.fasta.gz"/>
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49 <output name="json">
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50 <assert_contents>
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51 <has_text_matching expression="ref-S315T"/>
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52 </assert_contents>
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53 </output>
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54 </test>
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55 </tests>
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56 <help>
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57 @ATTRIBUTION@
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58 </help>
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59 <expand macro="citation" />
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60 </tool>