# HG changeset patch
# User iuc
# Date 1617056201 0
# Node ID 2c9f2a24f7a46f964352bc75e7293d5354c6ad2c
# Parent  29ec7b3a458b02eb499b7334c515ca3e22f7e775
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"

diff -r 29ec7b3a458b -r 2c9f2a24f7a4 migmap.xml
--- a/migmap.xml	Fri Nov 20 14:26:40 2020 +0000
+++ b/migmap.xml	Mon Mar 29 22:16:41 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="migmap" name="MiGMAP" version="@TOOL_VERSION@+galaxy1">
+<tool id="migmap" name="MiGMAP" version="@TOOL_VERSION@+galaxy2" profile="20.01">
     <description>mapper for full-length T- and B-cell repertoire sequencing
     </description>
     <macros>
@@ -16,9 +16,14 @@
 
 #if $input.is_of_type('fasta') :
     ln -s '$input' in.fa &&
-#else
+#else if $input.is_of_type('fasta.gz') :
+    ln -s '$input' in.fa.gz &&
+#else if $input.is_of_type('fastq') :
     ln -s '$input' in.fq &&
+#else if $input.is_of_type('fastq.gz') :
+    ln -s '$input' in.fq.gz
 #end if
+
 migmap 
     $allow_incomplete
     $allow_no_cdr3
@@ -91,6 +96,16 @@
             <output name="output" file="test_stop_codon.out"/>
         </test>
         <test>
+            <param name="input" value="test_stop_codon.fq.gz" ftype="fastqsanger.gz"/>
+            <param name="allow_noncoding" value="--allow-noncoding"/>
+            <param name="by_read" value="--by-read"/>
+            <param name="allow_noncanonical" value="--allow-noncanonical"/>
+            <param name="allow_no_cdr3" value="--allow-no-cdr3"/>
+            <param name="allow_incomplete" value="--allow-incomplete"/>
+            <param name="all_alleles" value="--all-alleles"/>
+            <output name="output" file="test_stop_codon.out" lines_diff="2"/>
+        </test>
+        <test>
             <param name="allow_noncoding" value="--allow-noncoding"/>
             <param name="by_read" value="--by-read"/>
             <param name="input" value="test_out_of_frame.fa"/>
diff -r 29ec7b3a458b -r 2c9f2a24f7a4 test-data/test_stop_codon.fq.gz
Binary file test-data/test_stop_codon.fq.gz has changed