Mercurial > repos > iuc > megan_daa2rma

changeset 1:10360f9989ee draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
author iuc
date Sat, 11 Dec 2021 11:51:34 +0000
parents e13ac00e6a4d
children 8a9cad43dcde
files daa2rma.xml macros.xml test-data/input1.sam test-data/input2.sam
diffstat 4 files changed, 24 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/daa2rma.xml	Tue Dec 07 10:16:58 2021 +0000
+++ b/daa2rma.xml	Sat Dec 11 11:51:34 2021 +0000
@@ -63,7 +63,10 @@
             <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"/>
@@ -76,7 +79,7 @@
         <data name="output" format="rma6"/>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="in" ftype="daa" value="input.daa"/>
             <output name="output" ftype="rma6">
                 <assert_contents>
@@ -84,7 +87,7 @@
                 </assert_contents>
             </output>
        </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="in" ftype="daa" value="input.daa"/>
             <param name="longReads" value="true"/>
             <param name="minScore" value="25.0"/>
@@ -100,7 +103,7 @@
     <help>
 **What it does**
 
-Computes a MEGAN RMA (RealMedia Audio) file from a DIOMAND DAA file, a proprietary file format developed by PowerISO Computing
+Generates a MEGAN RMA (RealMedia Audio) file from a DIAMOND DAA file, a proprietary file format developed by PowerISO Computing
 for disk image files.  MEGAN uses an update of the original RMA file format known as RMA6.
     </help>
     <expand macro="citations"/>
--- a/macros.xml	Tue Dec 07 10:16:58 2021 +0000
+++ b/macros.xml	Sat Dec 11 11:51:34 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">
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1.sam	Sat Dec 11 11:51:34 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input2.sam	Sat Dec 11 11:51:34 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