Mercurial > repos > iuc > abricate
changeset 10:c2ef298da409 draft default tip
"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 |
| parents | 3f3e247c053d |
| children | |
| files | abricate.xml abricate_list.xml abricate_summary.xml macros.xml test-data/output_summary.txt |
| diffstat | 5 files changed, 82 insertions(+), 9 deletions(-) [+] |
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--- a/abricate.xml Tue Apr 06 08:54:46 2021 +0000 +++ b/abricate.xml Thu Apr 15 18:21:41 2021 +0000 @@ -1,17 +1,12 @@ -<tool id="abricate" name="ABRicate" version="@VERSION@"> +<tool id="abricate" name="ABRicate" version="@VERSION@" profile="@PROFILE@"> <description> Mass screening of contigs for antimicrobial and virulence genes </description> - <edam_topics> - <edam_topic>topic_0622</edam_topic> - <edam_topic>topic_3301</edam_topic> - </edam_topics> - <edam_operations> - <edam_operation>operation_3482</edam_operation> - </edam_operations> <macros> <import>macros.xml</import> </macros> + <expand macro='xrefs'/> + <expand macro='edam_ontology'/> <expand macro="requirements" /> <expand macro="version_command" />
--- a/abricate_list.xml Tue Apr 06 08:54:46 2021 +0000 +++ b/abricate_list.xml Thu Apr 15 18:21:41 2021 +0000 @@ -1,10 +1,12 @@ -<tool id="abricate_list" name="ABRicate List" version="@VERSION@"> +<tool id="abricate_list" name="ABRicate List" version="@VERSION@" profile="@PROFILE@"> <description> List all of abricate's available databases. </description> <macros> <import>macros.xml</import> </macros> + <expand macro='xrefs'/> + <expand macro='edam_ontology'/> <expand macro="requirements" /> <expand macro="version_command" />
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abricate_summary.xml Thu Apr 15 18:21:41 2021 +0000 @@ -0,0 +1,56 @@ +<tool id="abricate_summary" name="ABRicate Summary" version="@VERSION@" profile="@PROFILE@"> + <description> + Combine ABRicate results into a simple matrix of gene presence/absence + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro='xrefs'/> + <expand macro='edam_ontology'/> + <expand macro="requirements" /> + <expand macro="version_command" /> + + <command detect_errors="exit_code"><![CDATA[ + mkdir reports && + #import re + #for report in $abricate_reports + #set $safename = re.sub('[^\w\-_\.]', '_', $report.element_identifier) + ln -s '$report' 'reports/$safename' && + #end for + cd reports/ && + abricate --summary * + > '$summary' + ]]></command> + + <inputs> + <param name="abricate_reports" type="data" multiple="true" format="tabular" label="Abricate output reports to summarize"/> + </inputs> + + <outputs> + <data name="summary" format="tabular"/> + </outputs> + + <tests> + <test> + <param name="abricate_reports" value="output_db-card.txt,output_db-megares.txt"/> + <output name="summary" ftype="tabular" file="output_summary.txt" /> + </test> + </tests> + + <help><![CDATA[ +**What it does** + +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. + +**Example Output** + +:: + + #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) + 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 + 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 . . . . . . . . . + + ]]></help> + + <expand macro="citations"/> +</tool>
--- a/macros.xml Tue Apr 06 08:54:46 2021 +0000 +++ b/macros.xml Thu Apr 15 18:21:41 2021 +0000 @@ -11,6 +11,23 @@ </xml> <token name="@VERSION@">1.0.1</token> + <token name="@PROFILE@">20.01</token> + + <xml name="edam_ontology"> + <edam_topics> + <edam_topic>topic_0622</edam_topic> + <edam_topic>topic_3301</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_3482</edam_operation> + </edam_operations> + </xml> + + <xml name="xrefs"> + <xrefs> + <xref type='bio.tools'>ABRicate</xref> + </xrefs> + </xml> <xml name="citations"> <citations>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_summary.txt Thu Apr 15 18:21:41 2021 +0000 @@ -0,0 +1,3 @@ +#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) +output_db-card.txt 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 +output_db-megares.txt 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 . . . . . . . . .