# HG changeset patch
# User bvalot
# Date 1655382748 0
# Node ID a3cc35af36350fa805708b98364082355510e407
planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
diff -r 000000000000 -r a3cc35af3635 clamlst_import.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/clamlst_import.xml Thu Jun 16 12:32:28 2022 +0000
@@ -0,0 +1,56 @@
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+ pymlst
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+ claMLST -v
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+ claMLST import --force --no-prompt
+ #if $mlst
+ -m $mlst
+ #end if
+ $database '$search' &> $logfile
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+**What it does**
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+Import a classical MLST database from pubMLST
+Example :
+- Pseudomonas aeruginosa
+- Escherichia spp (mlst=achtman)
+
+**License and citation**
+
+This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
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diff -r 000000000000 -r a3cc35af3635 clamlst_search.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/clamlst_search.xml Thu Jun 16 12:32:28 2022 +0000
@@ -0,0 +1,183 @@
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+ pymlst
+ sed
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+ claMLST -v
+ '${mlst}'
+ #if $log
+ 2> '${logfile}'
+ #end if
+ ]]>
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+ log
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+ fasta
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+**What it does**
+
+Search ST number from pubMLST database
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+You can use
+- Genome assembly (blat search)
+- Raw data (kma search)
+
+**Options:**
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+ -i, --identity FLOAT Minimum identity to search gene (default=0.9).
+ -c, --coverage FLOAT Minimum coverage to search gene (default=0.95).
+ -r, --reads INTEGER Minimum reads coverage to search gene (default=10).
+ -f, --fasta FILENAME Write fasta file with gene allele.
+
+**License and citation**
+
+This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
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