# HG changeset patch
# User iuc
# Date 1639223514 0
# Node ID d326b943f5e2e681953b52434c20c86ce2651dda
# Parent  5be253dd3e08bc15932a13ef75fdd9a67e55a010
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"

diff -r 5be253dd3e08 -r d326b943f5e2 blast2rma.xml
--- a/blast2rma.xml	Tue Dec 07 10:17:22 2021 +0000
+++ b/blast2rma.xml	Sat Dec 11 11:51:54 2021 +0000
@@ -130,7 +130,10 @@
             <expand macro="long_reads_param"/>
             <expand macro="max_matches_per_read_param"/>
             <expand macro="classify_param"/>
-            <expand macro="blast_params"/>
+            <expand macro="min_score_param"/>
+            <expand macro="max_expected_param"/>
+            <expand macro="min_percent_identity_param"/>
+            <expand macro="top_percent_param"/>
             <expand macro="min_max_params"/>
             <expand macro="lca_params"/>
             <expand macro="read_assignment_mode_param"/>
@@ -200,7 +203,7 @@
     <help>
 **What it does**
 
-Computes MEGAN RMA files from BLAST (or similar) files.  Inputs consist of reads in fasta or fasqsanger format (gzip compressin
+Generates MEGAN RMA files from BLAST (or similar) files.  Inputs consist of reads in fasta or fasqsanger format (gzip compression
 is supported) and associated Blast files.  Each read file should have been used previously as the Blast input to produce the
 associated Blast file for this tool.
 
diff -r 5be253dd3e08 -r d326b943f5e2 macros.xml
--- a/macros.xml	Tue Dec 07 10:17:22 2021 +0000
+++ b/macros.xml	Sat Dec 11 11:51:54 2021 +0000
@@ -79,10 +79,16 @@
     <macro name="classify_param">
         <param argument="--classify" type="boolean" truevalue="--classify" falsevalue="" checked="true" label="Run classification algorithm?"/>
     </macro>
-    <macro name="blast_params">
+    <macro name="min_score_param">
         <param argument="--minScore" type="float" value="50.0" label="Minimum score"/>
+    </macro>
+    <macro name="max_expected_param">
         <param argument="--maxExpected" type="float" value="0.01" label="Maximum expected"/>
+    </macro>
+    <macro name="min_percent_identity_param">
         <param argument="--minPercentIdentity" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent identity"/>
+    </macro>
+    <macro name="top_percent_param">
         <param argument="--topPercent" type="float" value="10.0" min="0.0" max="100.0" label="Top percent"/>
     </macro>
     <macro name="min_max_params">
diff -r 5be253dd3e08 -r d326b943f5e2 test-data/input1.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1.sam	Sat Dec 11 11:51:54 2021 +0000
@@ -0,0 +1,5 @@
+@HD	VN:1.5	SO:unsorted	GO:query
+@PG	ID:1	PN:MALT	CL:--mode BlastN --matchScore 2 --mismatchScore -3 --setLambda 0.625 --setK 0.41 --alignmentType Local --inFile 13-1941-6_S4_L001_R1_600000_fastq_gz.fastq.gz --index /home/galaxy/tool-data/malt_index/AF2122-1 --output ./output.rma6 --numThreads 1 --memoryMode load --maxTables 0 --minBitScore 50.0 --maxExpected 1.0 --minPercentIdentity 0.0 --maxAlignmentsPerQuery 25 --maxAlignmentsPerRef 1 --topPercent 10.0 --minSupportPercent 0.001 --minSupport 0 --minPercentIdentityLCA 0.0 --maxSeedsPerFrame 100 --maxSeedsPerRef 20 --seedShift 1 --gapOpen 11 --gapExtend 1 --band 4 --alignments ./alignments_output.SAM.gz --format SAM --outAligned ./aligned_output.fna.gz --outUnaligned ./unaligned_output.fna.gz	DS:BlastN
+@RG	ID:1	PL:unknown	SM:unknown
+@CO	BlastN-like alignments
+@CO	Reporting AS: bitScore, ZR: rawScore, ZE: expected, ZI: percent identity, ZL: reference length
diff -r 5be253dd3e08 -r d326b943f5e2 test-data/input2.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input2.sam	Sat Dec 11 11:51:54 2021 +0000
@@ -0,0 +1,5 @@
+@HD	VN:1.5	SO:unsorted	GO:query
+@PG	ID:1	PN:MALT	CL:--mode BlastN --matchScore 2 --mismatchScore -3 --setLambda 0.625 --setK 0.41 --alignmentType Local --inFile 13-1941-6_S4_L001_R2_600000_fastq_gz.fastq.gz --index /home/galaxy/tool-data/malt_index/AF2122-1 --output ./output.rma6 --numThreads 1 --memoryMode load --maxTables 0 --minBitScore 50.0 --maxExpected 1.0 --minPercentIdentity 0.0 --maxAlignmentsPerQuery 25 --maxAlignmentsPerRef 1 --topPercent 10.0 --minSupportPercent 0.001 --minSupport 0 --minPercentIdentityLCA 0.0 --maxSeedsPerFrame 100 --maxSeedsPerRef 20 --seedShift 1 --gapOpen 11 --gapExtend 1 --band 4 --alignments ./alignments_output.SAM.gz --format SAM --outAligned ./aligned_output.fna.gz --outUnaligned ./unaligned_output.fna.gz	DS:BlastN
+@RG	ID:1	PL:unknown	SM:unknown
+@CO	BlastN-like alignments
+@CO	Reporting AS: bitScore, ZR: rawScore, ZE: expected, ZI: percent identity, ZL: reference length