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changeset 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
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(-) [+]
line wrap: on
line diff
--- 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	.	.	.	.	.	.	.	.	.