--- a/lastdb.xml	Fri Nov 13 09:05:49 2020 +0000
+++ b/lastdb.xml	Wed Mar 24 22:36:50 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="last_db" name="LASTdb" version="@LAST_CONDA_VERSION@+galaxy1" profile="18.01">
+<tool id="last_db" name="LASTdb" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01">
 
     <description>prepares sequences for subsequent comparison and alignment using lastal.</description>
 
@@ -11,15 +11,22 @@
     </requirements>
 
     <command detect_errors="exit_code"><![CDATA[
-        lastdb
+        set -e -o pipefail; 
 
-        #if $input_files.ext == 'fasta'
+        #if $input_files.ext.endswith('.gz')
+        zcat 
+        #else
+        cat 
+        #end if
+        '$input_files' | lastdb
+
+        #if $input_files.ext.startswith('fasta')
             -Q 0
-        #else if $input_files.ext == 'fastqsanger'
+        #else if $input_files.ext.startswith('fastqsanger')
             -Q 1
-        #else if $input_files.ext == 'fastqsolexa'
+        #else if $input_files.ext.startswith('fastqsolexa')
             -Q 2
-        #else if $input_files.ext == 'fastqillumina'
+        #else if $input_files.ext.startswith('fastqillumina')
             -Q 3
         #end if
         $lastdb.sequences_type.protein 
@@ -29,14 +36,16 @@
         -S $lastdb.lastdb_advanced.S
         -u $lastdb.lastdb_advanced.seeds.u
         -w $lastdb.lastdb_advanced.seeds.w
-        -W $lastdb.lastdb_advanced.seeds.W 
+        #if $lastdb.lastdb_advanced.seeds.W
+            -W $lastdb.lastdb_advanced.seeds.W
+        #end if
         -m $lastdb.lastdb_advanced.seeds.m 
         -i $lastdb.lastdb_advanced.i 
         -C $lastdb.lastdb_advanced.C 
         -s \${GALAXY_MEMORY_MB:-2G}
         -P \${GALAXY_SLOTS:-1}        
         'lastdb' 
-        '$input_files'
+        
 
         &&
 
@@ -45,7 +54,7 @@
     ]]></command>
 
     <inputs>
-        <param name="input_files" type="data" format="fasta,fastqsanger,fastqsolexa,fastqillumina" label="Reference(s) input files" />
+        <param name="input_files" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Reference(s) input files" />
         <section name="lastdb" title="Lastdb arguments" expanded="true">
             <conditional name="sequences_type">
                 <param name="protein" type="select" multiple="false" label="The sequences are :">
@@ -81,7 +90,7 @@
                 </param>
 
                 <conditional name="seeds">
-                    <param argument="-u" type="select" multiple="false" label="Specify a seeding scheme.">
+                    <param argument="-u" type="select" multiple="false" optional="true" label="Specify a seeding scheme.">
                         <option value="BISF">BISF</option>
                         <option value="BISR">BISR</option>
                         <option value="MAM4">MAM4</option>
@@ -134,7 +143,7 @@
 
     <tests>
         <test>
-            <param name="input_files" value="humanMito.fa" ftype="fasta"/>
+            <param name="input_files" value="humanMito.fa.gz" ftype="fasta.gz"/>
             <section name="lastdb">
                 <section name="repeats">
                     <param name="uppercase" value="0"/>
@@ -145,7 +154,7 @@
             <output name="outfile" compare="contains" file="humdb.lastdb" ftype="lastdb">
                 <extra_files type="file" value="humdb.bck" name="lastdb.bck" compare="sim_size" delta="1"/>
                 <extra_files type="file" value="humdb.des" name="lastdb.des"/>
-                <extra_files type="file" value="humdb.prj" name="lastdb.prj"/>
+                <extra_files type="file" value="humdb.prj" name="lastdb.prj" compare="sim_size" delta="2"/>
                 <extra_files type="file" value="humdb.sds" name="lastdb.sds"/>
                 <extra_files type="file" value="humdb.ssp" name="lastdb.ssp" compare="sim_size" delta="1"/>
                 <extra_files type="file" value="humdb.suf" name="lastdb.suf" compare="sim_size" delta="1"/>
@@ -159,6 +168,10 @@
                     <param name="protein" value="-p"/> 
                 </conditional>
             </section>
+            <section name="lastdb_advanced">
+                <conditional name="seeds">
+                    <param name="u" value="MURPHY10"/>
+            </section>
             <output name="outfile" compare="contains" file="hedgdb.lastdb" ftype="lastdb">
                 <extra_files type="file" value="hedgdb.bck" name="lastdb.bck" compare="sim_size" delta="1"/>
                 <extra_files type="file" value="hedgdb.des" name="lastdb.des"/>
@@ -170,7 +183,7 @@
             </output>
         </test>
         <test>
-            <param name="input_files" value="humanMito.fq" ftype="fastqsanger"/>
+            <param name="input_files" value="humanMito.fq.gz" ftype="fastqsanger.gz"/>
             <section name="lastdb">
                 <param name="Q" value="1"/>
                 <section name="repeats">
@@ -182,7 +195,7 @@
             <output name="outfile" compare="contains" file="hedgdb.lastdb" ftype="lastdb">
                 <extra_files type="file" value="humdb-sanger.bck" name="lastdb.bck" compare="sim_size" delta="1"/>
                 <extra_files type="file" value="humdb-sanger.des" name="lastdb.des"/>
-                <extra_files type="file" value="humdb-sanger.prj" name="lastdb.prj" lines_diff="1"/>
+                <extra_files type="file" value="humdb-sanger.prj" name="lastdb.prj" lines_diff="2"/>
                 <extra_files type="file" value="humdb-sanger.sds" name="lastdb.sds"/>
                 <extra_files type="file" value="humdb-sanger.ssp" name="lastdb.ssp" compare="sim_size" delta="1"/>
                 <extra_files type="file" value="humdb-sanger.suf" name="lastdb.suf" compare="sim_size" delta="1"/>