# HG changeset patch
# User iuc
# Date 1585576900 14400
# Node ID 20bef04b52721ff2c4d263cf8c105a7db189f1a0
# Parent  60ed1c94f58402051aa06463f5e5b9a1ccc9cc67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 03afe9e2a97f86f13041214639112a80e9765a71"

diff -r 60ed1c94f584 -r 20bef04b5272 kc-align.xml
--- a/kc-align.xml	Fri Mar 27 15:00:09 2020 -0400
+++ b/kc-align.xml	Mon Mar 30 10:01:40 2020 -0400
@@ -1,6 +1,6 @@
-<tool id="kc-align" name="Kc-Align" version="0.1.2" python_template_version="3.5">
+<tool id="kc-align" name="Kc-Align" version="0.1.3" python_template_version="3.5">
     <requirements>
-        <requirement type="package" version="0.5.8">kcalign</requirement>
+        <requirement type="package" version="0.5.9">kcalign</requirement>
         <requirement type="package" version="3.2.2">kalign3</requirement>
     </requirements>
     <command detect_errors="exit_code">
@@ -13,6 +13,7 @@
                 --start $position.start
                 --end $position.end
             #end if
+            $compress
     ]]></command>
     <inputs>
         <param name="reference" type="data" format="fasta" label="Reference Sequence" help="Single FASTA reference sequence to be aligned" />
@@ -33,6 +34,7 @@
             <when value="mixed" >
             </when>
         </conditional>
+        <param name="compress" type="boolean" truevalue="--compress" falsevalue="" label="Compress" help="Compress identical sequences" />
     </inputs>
     <outputs>
         <data name="fasta" format="fasta" from_work_dir="codon_align.fasta" label="${outname}.fasta" />
diff -r 60ed1c94f584 -r 20bef04b5272 test-data/kc-align.fasta
--- a/test-data/kc-align.fasta	Fri Mar 27 15:00:09 2020 -0400
+++ b/test-data/kc-align.fasta	Mon Mar 30 10:01:40 2020 -0400
@@ -1,4 +1,4 @@
->NC_045512.2
+>NC_045512.2 Wuhan seafood market pneumonia virus isolate Wuhan-Hu-1, complete genome
 ATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACC
 AGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGAC
 AAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCC
@@ -63,7 +63,7 @@
 ATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGC
 TGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGAC
 TCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA
->MT019531.1
+>MT019531.1 Severe acute respiratory syndrome coronavirus 2 isolate BetaCoV/Wuhan/IPBCAMS-WH-03/2019, complete genome
 ATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACC
 AGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGAC
 AAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCC
@@ -128,7 +128,7 @@
 ATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGC
 TGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGAC
 TCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA
->MN996528.1
+>MN996528.1 Severe acute respiratory syndrome coronavirus 2 isolate WIV04, complete genome
 ATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACC
 AGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGAC
 AAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCC
@@ -193,7 +193,7 @@
 ATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGC
 TGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGAC
 TCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA
->MT019532.1
+>MT019532.1 Severe acute respiratory syndrome coronavirus 2 isolate BetaCoV/Wuhan/IPBCAMS-WH-04/2019, complete genome
 ATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACC
 AGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGAC
 AAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCC