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comparison 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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9:3f3e247c053d 10:c2ef298da409
1 <tool id="abricate_summary" name="ABRicate Summary" version="@VERSION@" profile="@PROFILE@">
2 <description>
3 Combine ABRicate results into a simple matrix of gene presence/absence
4 </description>
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro='xrefs'/>
9 <expand macro='edam_ontology'/>
10 <expand macro="requirements" />
11 <expand macro="version_command" />
12
13 <command detect_errors="exit_code"><![CDATA[
14 mkdir reports &&
15 #import re
16 #for report in $abricate_reports
17 #set $safename = re.sub('[^\w\-_\.]', '_', $report.element_identifier)
18 ln -s '$report' 'reports/$safename' &&
19 #end for
20 cd reports/ &&
21 abricate --summary *
22 > '$summary'
23 ]]></command>
24
25 <inputs>
26 <param name="abricate_reports" type="data" multiple="true" format="tabular" label="Abricate output reports to summarize"/>
27 </inputs>
28
29 <outputs>
30 <data name="summary" format="tabular"/>
31 </outputs>
32
33 <tests>
34 <test>
35 <param name="abricate_reports" value="output_db-card.txt,output_db-megares.txt"/>
36 <output name="summary" ftype="tabular" file="output_summary.txt" />
37 </test>
38 </tests>
39
40 <help><![CDATA[
41 **What it does**
42
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.
44
45 **Example Output**
46
47 ::
48
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)
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
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 . . . . . . . . .
52
53 ]]></help>
54
55 <expand macro="citations"/>
56 </tool>