From 26965174db04c0f57ea305da5a3f824470a82eaa Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?=
 <gallardo@informatik.uni-freiburg.de>
Date: Thu, 31 Aug 2023 11:01:34 +0200
Subject: [PATCH] Update files

---
 tools/rna_tools/sortmerna/macros.xml    |  4 ++--
 tools/rna_tools/sortmerna/sortmerna.xml | 10 +++++++---
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/tools/rna_tools/sortmerna/macros.xml b/tools/rna_tools/sortmerna/macros.xml
index 99c88fd7cb..ccefc0de84 100644
--- a/tools/rna_tools/sortmerna/macros.xml
+++ b/tools/rna_tools/sortmerna/macros.xml
@@ -8,8 +8,8 @@
         </requirements>
     </xml>
     <xml name="db_prep">
-        <param name="seed_length" type="integer" min="0" max="100" value="18" label="Seed length for database indexing" help="(-L)"/>
-        <param name="max_pos" type="integer" min="0" max="100000" value="10000" label="Maximum number of positions to store for each k-mer for database indexing" help="With 0, all positions are stored (--max_pos)"/>
+        <param name="seed_length" argument="-L" type="integer" min="0" max="100" value="18" label="Seed length" help="Seed length for database indexing"/>
+        <param argument="--max_pos" type="integer" min="0" max="100000" value="10000" label="Maximum number of positions to store for each k-mer for database indexing" help="With 0, all positions are stored"/>
     </xml>
     <xml name="reads_macro">
         <param argument="--reads" type="data" format="fasta,fastq,fastq.gz" label="Querying sequences"/>
diff --git a/tools/rna_tools/sortmerna/sortmerna.xml b/tools/rna_tools/sortmerna/sortmerna.xml
index 112fa8cce6..6d84f0a687 100644
--- a/tools/rna_tools/sortmerna/sortmerna.xml
+++ b/tools/rna_tools/sortmerna/sortmerna.xml
@@ -30,6 +30,8 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
     
     mkdir -p './aligned' &&
     mkdir -p './kvdb_folder' &&
+    mkdir -p './idx_folder' &&
+    mkdir -p './readb_folder' &&
 
     sortmerna
         #for $i, $reference in enumerate($ref)
@@ -80,6 +82,8 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
         --threads \${GALAXY_SLOTS:-1}
         -m \${GALAXY_MEMORY_MB:-8192}
         --kvdb 'kvdb_folder'
+        --idx-dir 'idx_folder'
+        --readb 'readb_folder'
         #if $aligned_fastx.aligned_fastx_selector == '--fastx' and str($sequencing_type.sequencing_type_selector) == 'paired'
             --out2
         #end if
@@ -100,8 +104,8 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
                 <expand macro="reads_macro"/>
             </when>
             <when value="paired">
-                <param name="forward_reads" type="data" format="fasta,fastq,fastq.gz" label="Forward reads"/>
-                <param name="reverse_reads" type="data" format="fasta,fastq,fastq.gz" label="Reverse reads"/>
+                <param name="forward_reads" type="data" format="fasta,fastq,fastq.gz,fasta.gz" label="Forward reads"/>
+                <param name="reverse_reads" type="data" format="fasta,fastq,fastq.gz,fasta.gz" label="Reverse reads"/>
                 <expand macro="paired_type_macro"/>
             </when>
             <when value="interleaved">
@@ -136,7 +140,7 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
                 <expand macro="db_prep"/>
             </when>
             <when value="history">
-                <param name="database_name" type="data" format="fasta" multiple="true" label="rRNA databases" help="Your databases will be indexed first, which may take up to several minutes."/>
+                <param name="database_name" type="data" format="fasta,fasta.gz" multiple="true" label="rRNA databases" help="Your databases will be indexed first, which may take up to several minutes."/>
                 <expand macro="db_prep"/>
             </when>
         </conditional>