# HG changeset patch
# User iuc
# Date 1728908889 0
# Node ID 30e275ed0442290e6a1657ddcd84b5ae9a5793a4
# Parent  f1d1dafc836d7a00fa31ee3bde8465e00b42ed9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842

diff -r f1d1dafc836d -r 30e275ed0442 mapseq.xml
--- a/mapseq.xml	Tue Mar 12 21:22:41 2024 +0000
+++ b/mapseq.xml	Mon Oct 14 12:28:09 2024 +0000
@@ -1,7 +1,7 @@
 <tool id="mapseq" name="MAPseq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
     <description>sequence read classification designed to assign taxonomy and OTU classifications</description>
     <macros>
-        <token name="@TOOL_VERSION@">2.1.1</token>
+        <token name="@TOOL_VERSION@">2.1.1b</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <xrefs>
@@ -38,9 +38,11 @@
             ln -s '${ref_db.mscluster}' db.fasta.mscluster &&
             ln -s '${ref_db.mapseq2biom.otu_table}' db.otu &&
         #end if
-
         mapseq
         -nthreads \${GALAXY_SLOTS:-8}
+        #if str($seed) != ""
+            -seed '$seed'
+        #end if
         -tophits '$tophits'
         -topotus '$topotus'
         -minscore '$minscore'
@@ -107,6 +109,8 @@
             </when>
         </conditional>
                
+        <param argument="-seed" type="integer" label="Fix random seed" help="Sets a fixed integer seed value for random number generation, ensuring reproducible results" optional="true"/>
+
         <param argument="-tophits" type="integer" label="Top hits" help="Number of reference sequences to include in alignment phase"
                 value="20" min="1" max="200" />
                
@@ -154,6 +158,9 @@
             <param name="mscluster" value="mapseq_db/LSU_trimmed.fasta.mscluster"/>
             <param name="mapseq2biom" value="no"/>
             <output name="classifications" file="sequences.mapseq" sort="true"/>
+            <assert_command>
+                <has_text text="-seed" negate="true" />
+            </assert_command>
         </test>
         <test expect_num_outputs="1">
             <param name="db_source" value="history" />
@@ -162,6 +169,9 @@
             <param name="taxonomy" value="mapseq_db/slv_lsu_filtered2_trimmed.txt"/>
             <param name="mapseq2biom" value="no"/>
             <output name="classifications" file="sequences.mapseq" sort="true"/>
+            <assert_command>
+                <has_text text="-seed" negate="true" />
+            </assert_command>
         </test>
         <test expect_num_outputs="3">
             <param name="db_source" value="history" />
@@ -172,9 +182,13 @@
             <param name="mapseq2biom" value="yes"/>
             <param name="krona_input" value="no"/>
             <param name="otu_table" value="mapseq_db/test.otu" />
+            <param name="seed" value="12" />
             <output name="classifications" file="sequences.mapseq" sort="true"/>
             <output name="otu_tsv" file="mapseq2biom/tab-output_including_taxIDs.tabular" />
             <output name="otu_tsv_notaxid" file="mapseq2biom/tab-output_without_taxIDs.tabular" />
+            <assert_command>
+                <has_text text="-seed '12'" n="1" />
+            </assert_command>
         </test>
         <test expect_num_outputs="4">
             <param name="db_source" value="history" />
@@ -189,6 +203,9 @@
             <output name="otu_tsv" file="mapseq2biom/tab-output_including_taxIDs.tabular" />
             <output name="otu_tsv_notaxid" file="mapseq2biom/tab-output_without_taxIDs.tabular" />
             <output name="krona_format" file="mapseq2biom/krona_input.tabular" />
+            <assert_command>
+                <has_text text="-seed" negate="true" />
+            </assert_command>
         </test>
         <test expect_num_outputs="1">
             <param name="db_source" value="cached" />
@@ -196,6 +213,9 @@
             <param name="sequences" value="sequences.fasta"/>
             <param name="mapseq2biom" value="no"/>
             <output name="classifications" file="sequences.mapseq" sort="true"/>
+            <assert_command>
+                <has_text text="-seed" negate="true" />
+            </assert_command>
         </test>
         <test expect_num_outputs="3">
             <param name="db_source" value="cached" />
@@ -206,6 +226,9 @@
             <output name="classifications" file="sequences.mapseq" sort="true"/>
             <output name="otu_tsv" file="mapseq2biom/tab-output_including_taxIDs.tabular" />
             <output name="otu_tsv_notaxid" file="mapseq2biom/tab-output_without_taxIDs.tabular" />
+            <assert_command>
+                <has_text text="-seed" negate="true" />
+            </assert_command>
         </test>
         <test expect_num_outputs="4">
             <param name="db_source" value="cached" />
@@ -213,10 +236,14 @@
             <param name="sequences" value="sequences.fasta"/>
             <param name="mapseq2biom" value="yes"/>
             <param name="krona_input" value="yes"/>
+            <param name="seed" value="12" />
             <output name="classifications" file="sequences.mapseq" sort="true"/>
             <output name="otu_tsv" file="mapseq2biom/tab-output_including_taxIDs.tabular" />
             <output name="otu_tsv_notaxid" file="mapseq2biom/tab-output_without_taxIDs.tabular" />
             <output name="krona_format" file="mapseq2biom/krona_input.tabular" />
+            <assert_command>
+                <has_text text="-seed '12'" n="1" />
+            </assert_command>
         </test>
     </tests>
 
@@ -289,6 +316,10 @@
 -------
 * `Apache-2.0 license <https://raw.githubusercontent.com/EBI-Metagenomics/pipeline-v5/master/LICENSE>`_
     ]]></help>
+    <creator>
+        <person givenName="Rand" familyName="Zoabi" url="https://github.com/RZ9082"/>
+        <person givenName="Paul" familyName="Zierep" url="https://github.com/paulzierep"/>
+    </creator>
     <citations>
         <citation type="doi">
             10.1093/bioinformatics/btx517
diff -r f1d1dafc836d -r 30e275ed0442 test-data/sequences.mapseq
--- a/test-data/sequences.mapseq	Tue Mar 12 21:22:41 2024 +0000
+++ b/test-data/sequences.mapseq	Mon Oct 14 12:28:09 2024 +0000
@@ -1,4 +1,3 @@
-# mapseq v1.2.6 (Jan 20 2023)
 #query	dbhit	bitscore	identity	matches	mismatches	gaps	query_start	query_end	dbhit_start	dbhit_end	strand		taxonomy.txt	
 ERR2407324.4-10333.Pue.782.huma-3-1	CP011466.3186026.3188977	48	0.698630154132843	102	41	3	0	146	1156	1299	-		sk__Eukaryota;k__Fungi;p__Ascomycota;c__Saccharomycetes;o__Saccharomycetales;f__;g__;s__	
 ERR2407324.6-10333.Pue.782.huma-5-1	CP011466.3186026.3188977	82	0.8026315569877625	122	28	2	0	150	1147	1299	-		sk__Eukaryota;k__Fungi;p__Ascomycota;c__Saccharomycetes;o__Saccharomycetales;f__;g__;s__