# HG changeset patch
# User iuc
# Date 1625855700 0
# Node ID d0847fe9b44341f4ac34438fc353925dc9af5e43
# Parent  c2228166c035b807ea0efd4cf61ffd182c4d4354
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 18de4aa9ba00124b1b3e3afe14219e46931e58a9"

diff -r c2228166c035 -r d0847fe9b443 emboss_fuzznuc.xml
--- a/emboss_fuzznuc.xml	Fri Nov 20 16:49:40 2020 +0000
+++ b/emboss_fuzznuc.xml	Fri Jul 09 18:35:00 2021 +0000
@@ -1,11 +1,35 @@
-<tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="5.0.2">
+<tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="5.0.3">
   <description>Nucleic acid pattern search</description>
   <macros>
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements" />
   <code file="emboss_format_corrector.py" />
-  <command>fuzznuc -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto</command>
+  <command><![CDATA[
+    fuzznuc
+
+    -sequence '$input1'
+    $seq_qualifiers.sreverse1 $seq_qualifiers.snucleotide1 $seq_qualifiers.sprotein1 $seq_qualifiers.slower1 $seq_qualifiers.supper1
+    #if $seq_qualifiers.sbegin1
+      -sbegin1 '$seq_qualifiers.sbegin1'
+    #end if
+    #if $seq_qualifiers.send1
+      -send1 '$seq_qualifiers.send1'
+    #end if
+
+    -outfile '$out_file1'
+    $out_qualifiers.raccshow2 $out_qualifiers.rdesshow2 $out_qualifiers.rscoreshow2 $out_qualifiers.rusashow2
+    #if $out_qualifiers.rmaxall2
+      -rmaxall2 '$out_qualifiers.rmaxall2'
+    #end if
+    #if $out_qualifiers.rmaxseq2
+      -rmaxseq2 '$out_qualifiers.rmaxseq2'
+    #end if
+
+    -pattern '$pattern' -pmismatch '$mismatch' -rformat2 '$out_format1' -auto
+
+    -complement '$complement'
+  ]]></command>
   <inputs>
     <param name="input1" type="data" format="fasta" label="Sequences" />
     <param name="pattern" type="text" value="" label="Search pattern">
@@ -42,6 +66,26 @@
       <option value="table">Table</option>
       <option value="tagseq">TagSeq</option>
     </param>
+
+    <section name="seq_qualifiers" title="Sequence associated qualifiers">
+      <param type="integer" argument="-sbegin1" optional="true" label="Start of each sequence to be used"/>
+      <param type="integer" argument="-send1" optional="true" label="End of each sequence to be used"/>
+      <param type="boolean" argument="-sreverse1" truevalue="-sreverse1 Y" falsevalue="" label="Reverse (if DNA)"/>
+      <param type="boolean" argument="-snucleotide1" truevalue="-snucleotide1 Y" falsevalue="" label="Sequence is nucleotide"/>
+      <param type="boolean" argument="-sprotein1" truevalue="-sprotein1 Y" falsevalue="" label="Sequence is protein"/>
+      <param type="boolean" argument="-slower1" truevalue="-slower1 Y" falsevalue="" label="Make lower case"/>
+      <param type="boolean" argument="-supper1" truevalue="-supper1 Y" falsevalue="" label="Make upper case"/>
+    </section>
+
+    <section name="out_qualifiers" title="Outfile associated qualifiers">
+      <param type="boolean" argument="-raccshow2" truevalue="-raccshow2 Y" falsevalue="" label="Show accession number in the report"/>
+      <param type="boolean" argument="-rdesshow2" truevalue="-rdesshow2 Y" falsevalue="" label="Show description in the report"/>
+      <param type="boolean" argument="-rscoreshow2" truevalue="-rscoreshow2 Y" falsevalue="" label="Show the score in the report"/>
+      <param type="boolean" argument="-rusashow2" truevalue="-rusashow2 Y" falsevalue="" label="Show the full USA in the report"/>
+      <param type="integer" argument="-rmaxall2" optional="true" label="Maximum total hits to report"/>
+      <param type="integer" argument="-rmaxseq2" optional="true" label="Maximum hits to report for one sequence"/>
+    </section>
+
   </inputs>
   <outputs>
     <data name="out_file1" format="fuzznuc" />
@@ -55,6 +99,17 @@
       <param name="out_format1" value="excel"/>
       <output name="out_file1" file="emboss_fuzznuc_out.tabular"/>
     </test>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="pattern" value="AA"/>
+      <param name="mismatch" value="0"/>
+      <param name="complement" value="no"/>
+      <param name="out_format1" value="excel"/>
+      <param name="seq_qualifiers|supper1" value="true"/>
+      <param name="seq_qualifiers|sbegin1" value="100"/>
+      <param name="out_qualifiers|rmaxseq2" value="5"/>
+      <output name="out_file1" file="emboss_fuzznuc_out2.tabular"/>
+    </test>
   </tests>
   <help>
 .. class:: warningmark
diff -r c2228166c035 -r d0847fe9b443 test-data/emboss_fuzznuc_out2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_fuzznuc_out2.tabular	Fri Jul 09 18:35:00 2021 +0000
@@ -0,0 +1,6 @@
+SeqName	Start	End	Score	Strand	Pattern_name	Mismatch
+Sequence	157	158	2	+	pattern1	.
+Sequence	158	159	2	+	pattern1	.
+Sequence	181	182	2	+	pattern1	.
+Sequence	193	194	2	+	pattern1	.
+Sequence	196	197	2	+	pattern1	.