--- a/repeatmasker.xml	Tue Aug 18 09:39:33 2020 +0000
+++ b/repeatmasker.xml	Fri Dec 11 22:25:26 2020 +0000
@@ -1,31 +1,36 @@
-<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.9" profile="17.01">
+<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.1.1" profile="17.01">
   <description>screen DNA sequences for interspersed repeats and low complexity regions</description>
 
   <requirements>
-    <requirement type="package" version="4.0.9_p2">repeatmasker</requirement>
+    <requirement type="package" version="4.1.1">repeatmasker</requirement>
   </requirements>
 
   <command detect_errors="exit_code"><![CDATA[
     RM_PATH=\$(which RepeatMasker) &&
     if [ -z "\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\$PATH)" >&2 ; exit 1 ; fi &&
+
     RM_LIB_PATH=\$(dirname \$RM_PATH)/../share/RepeatMasker/Libraries &&
-    mkdir lib &&
-    export REPEATMASKER_LIB_DIR=\$(pwd)/lib &&
-      for file in \$(ls \$RM_LIB_PATH) ; do  ln -s \$RM_LIB_PATH/\$file lib/\$file ; done &&
-    #if $repeat_source.source_type == "repbase":
-      cp '${repeat_source.repbase_file}' 'lib/${repeat_source.repbase_file_name}' &&
+    #if $repeat_source.source_type == "dfam_up":
+      mkdir lib/ &&
+      ln -s '${repeat_source.dfam_lib}' lib/RepeatMaskerLib.h5 &&
+      RM_LIB_PATH=\$(pwd)/lib &&
     #end if
+
     ln -s '${input_fasta}' rm_input.fasta &&
+
     RepeatMasker -dir \$(pwd)
+    -libdir \$RM_LIB_PATH
     #if $repeat_source.source_type == "library":
       -lib '${repeat_source.repeat_lib}'
       -cutoff '${repeat_source.cutoff}'
-    #else if $repeat_source.source_type == "repbase":
+    #else if $repeat_source.source_type == "dfam":
       #if $repeat_source.species_source.species_from_list == 'yes':
-        $repeat_source.species_source.species_list
+        -species $repeat_source.species_source.species_list
       #else
         -species '${repeat_source.species_source.species_name}'
       #end if
+    #else if $repeat_source.source_type == "dfam_up":
+        -species '${repeat_source.species_name}'
     #end if
     -parallel \${GALAXY_SLOTS:-1}
     ${gff}
@@ -79,13 +84,12 @@
   <inputs>
     <param name="input_fasta" type="data" format="fasta" label="Genomic DNA" />
     <conditional name="repeat_source">
-      <param label="Repeat library source" name="source_type" type="select">
-        <option selected="true" value="repbase">RepBase</option>
+      <param label="Repeat library source" name="source_type" type="select" help="To use RepBase, choose 'Custom library of repeats' and select a fasta version of this non-free database.">
+        <option selected="true" value="dfam">DFam (curated only, bundled with RepeatMasker)</option>
+        <option value="dfam_up">DFam (full/specific version)</option>
         <option value="library">Custom library of repeats</option>
       </param>
-      <when value="repbase">
-        <param name="repbase_file" type="data" format="embl" label="RepBase (RMRBSeqs.embl) file" />
-        <param name="repbase_file_name" type="hidden" value="RMRBSeqs.embl"/> <!-- This is an ugly hack to allow testing with a fake repbase -->
+      <when value="dfam">
         <conditional name="species_source">
           <param label="Select species name from a list?" name="species_from_list" type="select">
             <option value="yes" selected="true">Yes</option>
@@ -93,40 +97,26 @@
           </param>
           <when value="yes">
             <param name="species_list" type="select" label="Species">
-              <option value="-species anopheles" selected="true">anopheles</option>
-              <option value="-species arabidopsis">arabidopsis</option>
-              <option value="-species artiodactyl">artiodactyl</option>
-              <option value="-species aspergillus">aspergillus</option>
-              <option value="-species carnivore">carnivore</option>
-              <option value="-species cat">cat</option>
-              <option value="-species chicken">chicken</option>
-              <option value="-species 'ciona intestinalis'">ciona intestinalis</option>
-              <option value="-species 'ciona savignyi'">ciona savignyi</option>
-              <option value="-species cow">cow</option>
-              <option value="-species danio">danio</option>
-              <option value="-species diatoaea">diatomea</option>
-              <option value="-species dog">dog</option>
-              <option value="-species drosophila">drosophila</option>
-              <option value="-species elegans">elegans</option>
-              <option value="-species fugu">fugu</option>
-              <option value="-species fungi" selected="true">fungi</option>
-              <option value="-species human">human</option>
-              <option value="-species maize">maize</option>
-              <option value="-species mammal">mammal</option>
-              <option value="-species mouse">mouse</option>
-              <option value="-species pig">pig</option>
-              <option value="-species rat">rat</option>
-              <option value="-species rice">rice</option>
-              <option value="-species rodentia">rodentia</option>
-              <option value="-species ruminantia">ruminantia</option>
-              <option value="-species wheat">wheat</option>
+              <option value="vertebrate">Vertebrate (other than below)</option>
+              <option value="mammal">Mammal (other than below)</option>
+              <option value="human" selected="true">Human</option>
+              <option value="rodent">Rodent</option>
+              <option value="mouse">Mouse</option>
+              <option value="rat">Rat</option>
+              <option value="danio">Danio (zebra fish)</option>
+              <option value="drosophila">Fruit fly (Drosophila melanogaster)</option>
+              <option value="elegans">Caenorhabditis elegans (nematode)</option>
             </param>
           </when>
           <when value="no">
-            <param name="species_name" type="text" value="homo sapiens" label="Repeat source species" help="Source species (or clade name) used to select repeats from RepBase" />
+            <param name="species_name" type="text" value="human" label="Repeat source species" help="Source species (or clade name) used to select repeats from DFam" />
           </when>
         </conditional>
       </when>
+      <when value="dfam_up">
+          <param name="dfam_lib" type="data" format="h5" label="DFam library" help="The full DFam library can be downloaded from https://www.dfam.org/releases/current/families/Dfam.h5.gz" />
+          <param name="species_name" type="text" value="human" label="Repeat source species" help="Source species (or clade name) used to select repeats from DFam" />
+      </when>
       <when value="library">
         <param name="repeat_lib" type="data" format="fasta" label="Custom library of repeats" />
         <param name="cutoff" type="integer" argument="-cutoff" value="225" label="Cutoff score for masking repeats" />
@@ -199,7 +189,6 @@
       <param name="input_fasta" value="small.fasta" ftype="fasta" />
       <param name="source_type" value="library" />
       <param name="gff" value="-gff" />
-      <!-- <param name="show" value="yes" /> -->
       <param name="keep_alignments" value="-ali" />
       <param name="poly" value="-poly" />
       <param name="repeat_lib" value="repeats.fasta" ftype="fasta" />
@@ -213,14 +202,22 @@
     </test>
     <test expect_num_outputs="4">
       <param name="input_fasta" value="small.fasta" ftype="fasta" />
-      <param name="source_type" value="repbase" />
-      <param name="repbase_file" value="fake_repbase.embl" />
-      <param name="repbase_file_name" value="fake.embl" />
-      <param name="species_list" value="anopheles" />
-      <output name="output_masked_genome" file="small.fasta.masked" />
-      <output name="output_table" file="small_repbase.fasta.stats" lines_diff="2" />
-      <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" />
-      <output name="output_log" file="small_repbase.fasta.log" lines_diff="2"/>
+      <param name="source_type" value="dfam" />
+      <param name="species_list" value="human" />
+      <output name="output_masked_genome" file="small_dfam.fasta.masked" />
+      <output name="output_table" file="small_dfam.fasta.stats" lines_diff="2" />
+      <output name="output_repeat_catalog" file="small_dfam.fasta.cat" lines_diff="2" />
+      <output name="output_log" file="small_dfam.fasta.log" lines_diff="2"/>
+    </test>
+    <test expect_num_outputs="4">
+      <param name="input_fasta" value="small.fasta" ftype="fasta" />
+      <param name="source_type" value="dfam_up" />
+      <param name="dfam_lib" value="Dfam_partial_test.h5" ftype="h5" />
+      <param name="species_name" value="rodent" />
+      <output name="output_masked_genome" file="small_dfam_up.fasta.masked" />
+      <output name="output_table" file="small_dfam_up.fasta.stats" lines_diff="2" />
+      <output name="output_repeat_catalog" file="small_dfam_up.fasta.cat" lines_diff="2" />
+      <output name="output_log" file="small_dfam_up.fasta.log" lines_diff="2"/>
     </test>
   </tests>
   <help><![CDATA[