# HG changeset patch
# User iuc
# Date 1630482341 0
# Node ID 7a4c104238aa6e704e60810c2e9d4e9e5a105525
# Parent d779062514e014c7f75a135db1cb6b4e38af24be
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
diff -r d779062514e0 -r 7a4c104238aa macro.xml
--- a/macro.xml Thu Jan 02 17:03:12 2020 +0000
+++ b/macro.xml Wed Sep 01 07:45:41 2021 +0000
@@ -1,147 +1,102 @@
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- mykrobe
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- 0.10.0
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+ mykrobe
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- #end if
- ]]>
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- $guess_sequence_method
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- $ignore_minor_calls
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- #if $ignore_filtered:
- --ignore_filtered '${ignore_filtered}'
- #end if
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- #if $model:
- --model '${model}'
- #end if
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- #if $ploidy:
- --ploidy '${ploidy}'
- #end if
- ]]>
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- 10.1038/ncomms10063
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+ 10.1038/ncomms10063
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diff -r d779062514e0 -r 7a4c104238aa mykrobe_genotype.xml
--- a/mykrobe_genotype.xml Thu Jan 02 17:03:12 2020 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,60 +0,0 @@
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- Antibiotic resistance predictions
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- macro.xml
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- '$json'
-]]>
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-@ATTRIBUTION@
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diff -r d779062514e0 -r 7a4c104238aa mykrobe_genotype_LOCAL_216918.xml
diff -r d779062514e0 -r 7a4c104238aa mykrobe_genotype_REMOTE_216918.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mykrobe_genotype_REMOTE_216918.xml Wed Sep 01 07:45:41 2021 +0000
@@ -0,0 +1,63 @@
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+ Antibiotic resistance predictions
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+ Mykrobe
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+ macro.xml
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+ '$json'
+]]>
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diff -r d779062514e0 -r 7a4c104238aa mykrobe_predict.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mykrobe_predict.xml.orig Wed Sep 01 07:45:41 2021 +0000
@@ -0,0 +1,154 @@
+<<<<<<< HEAD
+
+ Antibiotic resistance predictions
+=======
+
+ Antibiotic resistance predictions
+
+ Mykrobe
+
+>>>>>>> 84b0f9990 (add bio.tools IDs until M)
+
+ macro.xml
+
+
+<<<<<<< HEAD
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+>>>>>> 84b0f9990 (add bio.tools IDs until M)
+
+mykrobe predict
+--species '${select_species.species}'
+--panel '${select_species.panel}'
+
+#if $conf_percent_cutoff:
+ --conf_percent_cutoff '${conf_percent_cutoff}'
+#end if
+
+#if $min_depth:
+ --min_depth ${min_depth}
+#end if
+
+@shared_options@
+
+-q
+-t "\${GALAXY_SLOTS:-1}"
+
+#if $data_type.type in ["single", "paired"]:
+ #set read1 = $data_type.seq1
+ #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
+ #if $data_type.type == "single":
+ --sample '${read1_identifier}'
+ --seq '${read1}'
+ #else:
+ #set read2 = $data_type.seq2
+ #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
+ #set matches = difflib.SequenceMatcher(None, read1_identifier, read2_identifier).get_matching_blocks()
+ #set match = $matches[0]
+ #set identifier = re.sub('[^\s\w\-]', '_', str($read1_identifier[match.a:match.a + match.size]))
+ --sample '${identifier}'
+ --seq '${read1}' '${read2}'
+ #end if
+#elif $data_type.type == "collection":
+ #set identifier = re.sub('[^\s\w\-]', '_', str($data_type.collection1.element_identifier))
+ --sample '${identifier}'
+ --seq '${data_type.collection1.forward}' '${data_type.collection1.reverse}'
+#end if
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+--format '${format}'
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+> '$output']]>
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+ @ATTRIBUTION@
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diff -r d779062514e0 -r 7a4c104238aa test-data/reads.fastq.gz
Binary file test-data/reads.fastq.gz has changed