# HG changeset patch
# User iuc
# Date 1638573062 0
# Node ID 1930eb870dcadc0d9989cd24751faae903ab6fd6
# Parent  ad69d2a05c3cbe9f1325a259c8aeb1dd1b462115
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"

diff -r ad69d2a05c3c -r 1930eb870dca blast2lca.xml
--- a/blast2lca.xml	Wed Nov 24 21:52:36 2021 +0000
+++ b/blast2lca.xml	Fri Dec 03 23:11:02 2021 +0000
@@ -76,11 +76,11 @@
             <param argument="--showRanks" type="boolean" truevalue="--showRanks" falsevalue="" checked="true" label="Show taxonomic ranks?"/>
             <param argument="--officialRanksOnly" type="boolean" truevalue="--officialRanksOnly" falsevalue="" checked="true" label="Report only taxa that have an official rank?"/>
             <param  argument="--showTaxIds" type="boolean" truevalue="--showTaxIds" falsevalue="" checked="false" label="Report taxon ids rather than taxon names?"/>
-            <expand macro="common_blast_params"/>
+            <expand macro="blast_params"/>
             <param argument="--maxKeggPerRead" type="integer" value="4" label="Maximum number of KEGG assignments to report for a read"/>
             <param argument="--applyTopPercentKegg" type="boolean" truevalue="--applyTopPercentKegg" falsevalue="" checked="true" label="Apply top percent filter in KEGG KO analysis?"/>
             <param argument="--parseTaxonNames" type="boolean" truevalue="--parseTaxonNames" falsevalue="" checked="true" label="Apply top percent filter in KEGG KO analysis?"/>
-            <param argument="--mapDB" type="data" format="sqlite" optional="true" label="MEGAN mapping db"/>
+            <expand macro="mapdb_param"/>
             <param argument="--acc2taxa" type="data" format="sqlite" optional="true" label="Accession-to-Taxonomy mapping file"/>
             <param argument="--syn2taxa" type="data" format="sqlite" optional="true" label="Synonyms-to-Taxonomy mapping file"/>
             <param argument="--acc2kegg" type="data" format="sqlite" optional="true" label="Accession-to-KEGG mapping file"/>
@@ -136,8 +136,6 @@
 To perform this analysis, MEGAN uses a mapping of GI numbers to KO groups. Hence, if a KEGG-based analysis is desired, then
 the database that is used in the BLAST alignment must contain GI numbers.
     </help>
-    <citations>
-        <citation type="doi">https://doi.org/10.1101/050559</citation>
-    </citations>
+    <expand macro="citations"/>
 </tool>
 
diff -r ad69d2a05c3c -r 1930eb870dca macros.xml
--- a/macros.xml	Wed Nov 24 21:52:36 2021 +0000
+++ b/macros.xml	Fri Dec 03 23:11:02 2021 +0000
@@ -38,6 +38,18 @@
             </when>
         </conditional>
     </macro>
+    <macro name="long_reads_param">
+        <param argument="--longReads" type="boolean" truevalue="--longReads" falsevalue="" checked="false" label="Parse and analyse input reads as long reads?"/>
+    </macro>
+    <macro name="classification_options">
+        <option value="EC" selected="true">EC</option>
+        <option value="EGGNOG">EGGNOG</option>
+        <option value="GTDB">GTDB</option>
+        <option value="INTERPRO2GO">INTERPRO2GO</option>
+        <option value="KEGG">KEGG</option>
+        <option value="SEED">SEED</option>
+        <option value="Taxonomy">Taxonomy</option>
+    </macro>
     <macro name="blast_mode_options">
         <option value="Unknown" selected="true">Unknown</option>
         <option value="BlastN">BlastN</option>
@@ -45,12 +57,42 @@
         <option value="BlastX">BlastX</option>
         <option value="Classifier">Classifier</option>
     </macro>
-    <macro name="common_blast_params">
+    <macro name="classify_param">
+        <param argument="--classify" type="boolean" truevalue="--classify" falsevalue="" checked="true" label="Run classification algorithm?"/>
+    </macro>
+    <macro name="blast_params">
         <param argument="--minScore" type="float" value="50.0" label="Minimum score"/>
         <param argument="--maxExpected" type="float" value="0.01" label="Maximum expected"/>
         <param argument="--minPercentIdentity" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent identity"/>
         <param argument="--topPercent" type="float" value="10.0" min="0.0" max="100.0" label="Top percent"/>
     </macro>
+    <macro name="min_max_params">
+        <param argument="--minSupportPercent" type="float" value="0.05" min="0.0" max="100.0" label="Minimum support as percent of assigned reads" help="0 value ignores"/>
+        <param argument="--minSupport" type="integer" value="0" label="Minimum support" help="0 value ignores"/>
+        <param argument="--minPercentReadCover" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent of read length to be covered by alignments"/>
+        <param argument="--minPercentReferenceCover" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent of reference length to be covered by alignments"/>
+        <param argument="--minReadLength" type="integer" value="0" label="Minimum read length"/>
+    </macro>
+    <macro name="lca_params">
+        <param argument="--lcaAlgorithm" type="select" label="Select the LCA algorithm to use for taxonomic assignment">
+            <option value="naive" selected="true">naive</option>
+            <option value="weighted">weighted</option>
+            <option value="longReads">longReads</option>
+        </param>
+        <param argument="--lcaCoveragePercent" type="float" value="100.0" min="0.0" max="100.0" label="Percent for the LCA to cover"/>
+    </macro>
+    <macro name="read_assignment_mode_param">
+        <param argument="--readAssignmentMode" type="select" label="Select the read assignment mode">
+            <option value="alignedBases" selected="true">alignedBases</option>
+            <option value="readCount">readCount</option>
+        </param>
+    </macro>
+    <macro name="con_file_param">
+        <param argument="--conFile" type="data" format="txt" optional="true" label="File of contaminant taxa (one id or name per line)" help="Optional, no selection ignores"/>
+    </macro>
+    <macro name="mapdb_param">
+        <param argument="--mapDB" type="data" format="sqlite" optional="true" label="MEGAN mapping db" help="Optional, no selection ignores"/>
+    </macro>
     <xml name="sanitize_query" token_validinitial="string.printable">
         <sanitizer>
             <valid initial="@VALIDINITIAL@">
@@ -64,6 +106,8 @@
     </xml>
     <xml name="citations">
         <citations>
+            <citation type="doi">10.1038/nmeth.3176</citation>
+            <citation type="doi">10.1101/gr.120618.111</citation>
             <citation type="doi">10.1101/gr.5969107</citation>
         </citations>
     </xml>
diff -r ad69d2a05c3c -r 1930eb870dca test-data/daa2info_output1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/daa2info_output1.txt	Fri Dec 03 23:11:02 2021 +0000
@@ -0,0 +1,3 @@
+# Number of reads: 1
+# Alignment mode:  BLASTP
+# Is meganized:    false
diff -r ad69d2a05c3c -r 1930eb870dca test-data/daa2info_output2.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/daa2info_output2.txt	Fri Dec 03 23:11:02 2021 +0000
@@ -0,0 +1,19 @@
+# Number of reads: 1
+# Alignment mode:  BLASTP
+# Is meganized:    true
+# Classifications: Taxonomy
+# Meganization summary:
+## @Creator	DAA2Info
+## @CreationDate
+## @ContentType	Summary4
+## @Names	input
+## @BlastMode	BlastP
+## @Uids
+## @Sizes	1.0
+## @TotalReads	1
+## @AdditionalReads	0
+## Classifications:
+##  Taxonomy (1 classes)
+## @Algorithm	Taxonomy	merge
+## @Parameters	
+## 
diff -r ad69d2a05c3c -r 1930eb870dca test-data/daa2info_output_summary2.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/daa2info_output_summary2.txt	Fri Dec 03 23:11:02 2021 +0000
@@ -0,0 +1,16 @@
+@Creator	DAA2Info
+@CreationDate
+@ContentType	Summary4
+@Names	input
+@BlastMode	BlastP
+@Uids
+@Sizes	1
+@TotalReads	1
+@AdditionalReads	0
+@Algorithm	Taxonomy	merge
+@Parameters	
+@ColorTable	Fews8	White-Green
+TAX	-2	1
+END_OF_DATA_TABLE
+#SampleID	@Source
+input.daa	input.DAA
diff -r ad69d2a05c3c -r 1930eb870dca test-data/input.daa
Binary file test-data/input.daa has changed
diff -r ad69d2a05c3c -r 1930eb870dca test-data/input_meganized.daa
Binary file test-data/input_meganized.daa has changed
diff -r ad69d2a05c3c -r 1930eb870dca test-data/read_extractor_input.rma6
Binary file test-data/read_extractor_input.rma6 has changed
diff -r ad69d2a05c3c -r 1930eb870dca test-data/read_extractor_output.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/read_extractor_output.txt	Fri Dec 03 23:11:02 2021 +0000
@@ -0,0 +1,2 @@
+>sequence
+LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY