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annotate abricate_summary.xml @ 10:c2ef298da409 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 6285862fce2b3e298ef0333489392335091b5b0d"
author iuc
date Thu, 15 Apr 2021 18:21:41 +0000
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10
c2ef298da409 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 6285862fce2b3e298ef0333489392335091b5b0d"
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1 <tool id="abricate_summary" name="ABRicate Summary" version="@VERSION@" profile="@PROFILE@">
c2ef298da409 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 6285862fce2b3e298ef0333489392335091b5b0d"
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2 <description>
c2ef298da409 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 6285862fce2b3e298ef0333489392335091b5b0d"
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3 Combine ABRicate results into a simple matrix of gene presence/absence
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
c2ef298da409 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 6285862fce2b3e298ef0333489392335091b5b0d"
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8 <expand macro='xrefs'/>
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9 <expand macro='edam_ontology'/>
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10 <expand macro="requirements" />
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11 <expand macro="version_command" />
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c2ef298da409 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 6285862fce2b3e298ef0333489392335091b5b0d"
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13 <command detect_errors="exit_code"><![CDATA[
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14 mkdir reports &&
c2ef298da409 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 6285862fce2b3e298ef0333489392335091b5b0d"
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15 #import re
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16 #for report in $abricate_reports
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17 #set $safename = re.sub('[^\w\-_\.]', '_', $report.element_identifier)
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18 ln -s '$report' 'reports/$safename' &&
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19 #end for
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20 cd reports/ &&
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21 abricate --summary *
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22 > '$summary'
c2ef298da409 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 6285862fce2b3e298ef0333489392335091b5b0d"
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23 ]]></command>
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24
c2ef298da409 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 6285862fce2b3e298ef0333489392335091b5b0d"
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25 <inputs>
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26 <param name="abricate_reports" type="data" multiple="true" format="tabular" label="Abricate output reports to summarize"/>
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27 </inputs>
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c2ef298da409 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 6285862fce2b3e298ef0333489392335091b5b0d"
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29 <outputs>
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30 <data name="summary" format="tabular"/>
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31 </outputs>
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c2ef298da409 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 6285862fce2b3e298ef0333489392335091b5b0d"
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33 <tests>
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34 <test>
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35 <param name="abricate_reports" value="output_db-card.txt,output_db-megares.txt"/>
c2ef298da409 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 6285862fce2b3e298ef0333489392335091b5b0d"
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36 <output name="summary" ftype="tabular" file="output_summary.txt" />
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37 </test>
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38 </tests>
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c2ef298da409 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 6285862fce2b3e298ef0333489392335091b5b0d"
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40 <help><![CDATA[
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41 **What it does**
c2ef298da409 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 6285862fce2b3e298ef0333489392335091b5b0d"
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c2ef298da409 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 6285862fce2b3e298ef0333489392335091b5b0d"
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43 ABRicate can combine results into a simple matrix of gene presence/absence. An absent gene is denoted by '.' and a present gene is represented by its '%COVERAGE`. This can be individual abricate reports, or a combined one.
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44
c2ef298da409 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 6285862fce2b3e298ef0333489392335091b5b0d"
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45 **Example Output**
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c2ef298da409 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 6285862fce2b3e298ef0333489392335091b5b0d"
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47 ::
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48
c2ef298da409 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 6285862fce2b3e298ef0333489392335091b5b0d"
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49 #FILE NUM_FOUND AAC3 ANT(4')-Ib ANT3-DPRIME ANT4-PRIME APH3-PRIME ARLR ARLS BLAI BLAR BLAZ BLE DHAP ERMA ErmA FOSB LMRS MECA MECI MEPA MEPB MEPR MGRA NORA NORB PC1_beta-lactamase_(blaZ) RLMH Staphylococcus_aureus_FosB Staphylococcus_aureus_norA Staphylococcys_aureus_LmrS TET38 arlR arlS mecA mecI mecR1 mepA mepR mgrA tet(38)
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50 sample1 15 . 100.00 . . . . . . . . . . . 100.00;100.00 . . . . . . . . . . 100.00 . 100.00 99.91 100.00 . 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
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51 sample2 24 100.00 . 100.00;100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00;100.00 . 100.00 100.00 100.00;100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 . 100.00 . . . 100.00 . . . . . . . . .
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52
c2ef298da409 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 6285862fce2b3e298ef0333489392335091b5b0d"
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53 ]]></help>
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54
c2ef298da409 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 6285862fce2b3e298ef0333489392335091b5b0d"
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55 <expand macro="citations"/>
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56 </tool>