--- a/maker.xml	Thu Oct 19 15:41:42 2017 -0400
+++ b/maker.xml	Sun Jul 01 16:11:34 2018 -0400
@@ -1,11 +1,19 @@
 <?xml version="1.0"?>
-<tool id="maker" name="Maker" profile="16.04" version="@VERSION@">
+<tool id="maker" name="Maker" profile="16.04" version="@VERSION@.1">
     <description>genome annotation pipeline</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <command><![CDATA[
+        RM_LIB_PATH=\$(dirname \$(which RepeatMasker))/../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 $repeat_masking.repeat_source.source_type == "repbase":
+          cp '${repeat_masking.repeat_source.repbase_file}' 'lib/${repeat_masking.repeat_source.repbase_file_name}' &&
+        #end if
+
         maker -CTL
 
         &&
@@ -104,28 +112,41 @@
 #end if
 
 #-----Repeat Masking (leave values blank to skip repeat masking)
-#if $repeat_masking.repeatmasker.do_rm == 'simple'
-model_org=simple # select a model organism for RepBase masking in RepeatMasker
+#if $repeat_masking.repeat_source.source_type == 'repbase'
+
+#if $repeat_masking.repeat_source.species_source.species_from_list == 'yes'
+model_org=${repeat_masking.repeat_source.species_source.species_list}
+#else
+model_org=${repeat_masking.repeat_source.species_source.species_name}
+#end if
+
 rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker
-#else if $repeat_masking.repeatmasker.do_rm == 'lib'
+softmask=${repeat_masking.repeat_source.softmask} # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)
+
+#else if $repeat_masking.repeat_source.source_type == 'library'
 model_org= # select a model organism for RepBase masking in RepeatMasker
-rmlib=${repeat_masking.repeatmasker.rmlib} # provide an organism specific repeat library in fasta format for RepeatMasker
+rmlib=${repeat_masking.repeat_source.repeatmasker.rmlib} # provide an organism specific repeat library in fasta format for RepeatMasker
+
+#if $repeat_masking.repeat_source.repeat_protein
+repeat_protein=${repeat_masking.repeat_source.repeat_protein} # provide a fasta file of transposable element proteins for RepeatRunner
+#else
+repeat_protein= # provide a fasta file of transposable element proteins for RepeatRunner
+#end if
+#if $repeat_masking.repeat_source.rm_gff
+rm_gff=${repeat_masking.repeat_source.rm_gff} # pre-identified repeat elements from an external GFF3 file
+#else
+rm_gff= # pre-identified repeat elements from an external GFF3 file
+#end if
+
+softmask=${repeat_masking.repeat_source.softmask} # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)
+
 #else
 model_org= # select a model organism for RepBase masking in RepeatMasker
 rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker
-#end if
-#if $repeat_masking.repeat_protein
-repeat_protein=${repeat_masking.repeat_protein} # provide a fasta file of transposable element proteins for RepeatRunner
-#else
-repeat_protein= # provide a fasta file of transposable element proteins for RepeatRunner
+softmask=0 # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)
 #end if
-#if $repeat_masking.rm_gff
-rm_gff=${repeat_masking.rm_gff} # pre-identified repeat elements from an external GFF3 file
-#else
-rm_gff= # pre-identified repeat elements from an external GFF3 file
-#end if
+
 prok_rm=0 # forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no
-softmask=${repeat_masking.softmask} # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)
 
 #-----Gene Prediction
 #if $abinitio_gene_prediction.snaphmm
@@ -359,32 +380,69 @@
         </section>
 
         <section name="repeat_masking" title="Repeat masking" expanded="True">
-            <conditional name="repeatmasker">
-                <param name="do_rm" type="select" label="Enable repeat masking with RepeatMasker">
+            <conditional name="repeat_source">
+              <param label="Repeat library source" name="source_type" type="select">
+                <option selected="true" value="repbase">RepBase</option>
+                <option value="library">Custom library of repeats</option>
+                <option value="no">Disable repeat masking (not recommended)</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 -->
+                <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>
                     <option value="no">No</option>
-                    <option value="simple" selected="true">Yes, run RepeatMasker with default simple models</option>
-                    <option value="lib">Yes, use an organism specific repeat library (fasta)</option>
-                </param>
-                <!-- full repbase cannot be redistributed (for licensing reasons, see https://hpc.nih.gov/apps/repbase_license.html),
-                    using only the default maker base
-                    model_org is ignored and replaced by 'simple' if the full RepBase is not available.
-                    model_org=simple means maker will search using the simple models shipped by default
-                    Installing RepBase requires to replace files in the RepeatMasker installation dir
-                     -->
-                <when value="no"/>
-                <when value="simple"/>
-                <when value="lib">
-                    <param name="rmlib" type="data" format="fasta" label="Organism specific repeat library for RepeatMasker (fasta)"/>
-                </when>
+                  </param>
+                  <when value="yes">
+                    <param name="species_list" type="select" label="Species">
+                      <option value="anopheles" selected="true">anopheles</option>
+                      <option value="arabidopsis">arabidopsis</option>
+                      <option value="artiodactyl">artiodactyl</option>
+                      <option value="aspergillus">aspergillus</option>
+                      <option value="carnivore">carnivore</option>
+                      <option value="cat">cat</option>
+                      <option value="chicken">chicken</option>
+                      <option value="ciona intestinalis">ciona intestinalis</option>
+                      <option value="ciona savignyi">ciona savignyi</option>
+                      <option value="cow">cow</option>
+                      <option value="danio">danio</option>
+                      <option value="diatoaea">diatomea</option>
+                      <option value="dog">dog</option>
+                      <option value="drosophila">drosophila</option>
+                      <option value="elegans">elegans</option>
+                      <option value="fugu">fugu</option>
+                      <option value="fungi" selected="true">fungi</option>
+                      <option value="human">human</option>
+                      <option value="maize">maize</option>
+                      <option value="mammal">mammal</option>
+                      <option value="mouse">mouse</option>
+                      <option value="pig">pig</option>
+                      <option value="rat">rat</option>
+                      <option value="rice">rice</option>
+                      <option value="rodentia">rodentia</option>
+                      <option value="ruminantia">ruminantia</option>
+                      <option value="wheat">wheat</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" />
+                  </when>
+                </conditional>
+                <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/>
+              </when>
+              <when value="library">
+                <param name="repeat_protein" type="data" format="fasta" label="Transposable element protein sequences for RepeatRunner" optional="True" />
+                <param name="rm_gff" type="data" format="fasta" label="Pre-identified repeat elements from an external GFF file" optional="True" />
+                <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/>
+              </when>
+              <when value="no"/>
             </conditional>
-            <param name="repeat_protein" type="data" format="fasta" label="Transposable element protein sequences for RepeatRunner (fasta)" help="Leave empty to skip" optional="True"/>
-            <param name="rm_gff" type="data" format="gff" label="Pre-identified repeat elements from an external GFF file" help="Leave empty to skip" optional="True"/>
-            <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/>
         </section>
 
         <section name="gene_prediction" title="Other predictions" expanded="True">
             <param name="pred_gff" type="data" format="gff" label="Predictions from an external GFF3 file" optional="True"/>
-            <param name="model_gff" type="data" format="gff" label="Annotated gene models an external GFF3 file" help="annotation pass-through" optional="True"/>
+            <param name="model_gff" type="data" format="gff" label="Annotated gene models from an external GFF3 file" help="annotation pass-through" optional="True"/>
             <param name="trna" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Find tRNAs with tRNAscan"/>
             <param name="snoscan_rrna" type="data" format="fasta" label="rRNA file to have Snoscan find snoRNAs" optional="True"/>
         </section>
@@ -428,6 +486,7 @@
             <param name="genome" value="genome.fasta"/>
             <param name="est_evidences|est" value="est.fasta"/>
             <param name="est_evidences|est2genome" value="1"/>
+            <param name="repeat_masking|repeat_source|source_type" value="no"/>
             <output name="output_gff" file="annot.gff3"/>
             <output name="output_evidences" file="evidences.gff3" compare="sim_size"/>
         </test>
@@ -436,6 +495,7 @@
             <param name="organism_type" value="prokaryotic"/>
             <param name="est_evidences|est" value="est.fasta"/>
             <param name="est_evidences|est2genome" value="1"/>
+            <param name="repeat_masking|repeat_source|source_type" value="no"/>
             <output name="output_gff" file="annot_proc.gff3"/>
             <output name="output_evidences" file="evidences_proc.gff3" compare="sim_size"/>
         </test>
@@ -445,6 +505,7 @@
             <param name="reannotation|maker_gff" value="evidences.gff3"/>
             <param name="reannotation|est_pass" value="true"/>
             <param name="est_evidences|est2genome" value="1"/>
+            <param name="repeat_masking|repeat_source|source_type" value="no"/>
             <output name="output_gff" file="annot_reuse.gff3"/>
             <output name="output_evidences" file="evidences_reuse.gff3" compare="sim_size"/>
         </test>
@@ -455,6 +516,7 @@
             <param name="abinitio_gene_prediction|aug_prediction|augustus_species" value="human"/>
             <param name="est_evidences|est" value="est.fasta"/>
             <param name="est_evidences|est2genome" value="1"/>
+            <param name="repeat_masking|repeat_source|source_type" value="no"/>
             <output name="output_gff" file="annot_human.gff3" compare="sim_size"/>
             <output name="output_evidences" file="evidences_human.gff3" compare="sim_size"/>
         </test>
@@ -465,6 +527,7 @@
             <param name="abinitio_gene_prediction|aug_prediction|augustus_model" value="local.tar.gz" ftype="augustus"/>
             <param name="est_evidences|est" value="est.fasta"/>
             <param name="est_evidences|est2genome" value="1"/>
+            <param name="repeat_masking|repeat_source|source_type" value="no"/>
             <output name="output_gff" file="annot_model.gff3" compare="sim_size"/>
             <output name="output_evidences" file="evidences_model.gff3" compare="sim_size"/>
         </test>
@@ -472,10 +535,21 @@
             <param name="genome" value="genome.fasta"/>
             <param name="est_evidences|est" value="est.fasta"/>
             <param name="est_evidences|est2genome" value="1"/>
-            <param name="repeat_masking|repeatmasker|do_rm" value="no"/>
+            <param name="repeat_masking|repeat_source|source_type" value="no"/>
             <output name="output_gff" file="annot_norm.gff3"/>
             <output name="output_evidences" file="evidences_norm.gff3" compare="sim_size"/>
         </test>
+        <test>
+            <param name="genome" value="genome.fasta"/>
+            <param name="est_evidences|est" value="est.fasta"/>
+            <param name="est_evidences|est2genome" value="1"/>
+            <param name="repeat_masking|repeat_source|source_type" value="repbase"/>
+            <param name="repeat_masking|repeat_source|repbase_file" value="fake_repbase.embl" />
+            <param name="repeat_masking|repeat_source|repbase_file_name" value="fake.embl" />
+            <param name="repeat_masking|repeat_source|species_list" value="anopheles" />
+            <output name="output_gff" file="annot_repbase.gff3"/>
+            <output name="output_evidences" file="evidences_norm.gff3" compare="sim_size"/>
+        </test>
     </tests>
     <help><![CDATA[
         MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER's inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources.