--- a/datamanager_create_reference.xml	Mon Jan 04 15:55:00 2016 -0500
+++ b/datamanager_create_reference.xml	Wed Oct 18 16:55:57 2017 -0400
@@ -1,19 +1,19 @@
-<tool id="data_manager_defuse_reference" name="DeFuse Reference DataManager" version="1.6.1" tool_type="manage_data">
+<tool id="data_manager_defuse_reference" name="DeFuse Reference DataManager" version="@DEFUSE_VERSION@.1" tool_type="manage_data">
  <description>create a defuse reference from Ensembl and UCSC sources</description>
- <requirements>
-  <requirement type="package" version="0.6.1">defuse</requirement>
-  <requirement type="package" version="0.1.18">samtools</requirement>
-  <requirement type="package" version="1.0.0">bowtie</requirement>
-  <requirement type="package" version="2013-05-09">gmap</requirement>
-  <requirement type="package" version="latest">kent</requirement>
- </requirements>
- <command interpreter="python"> datamanager_create_reference.py 
-    --dbkey $genome.ensembl_genome_version 
-    --description "$genome.ensembl_prefix $genome.ensembl_genome_version ($genome.ucsc_genome_version)"
-    --defuse_config $defuse_config
-    --defuse_script $defuse_script
-    $out_file
- </command>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <expand macro="defuse_requirement" />
+    </requirements>
+    <command interpreter="python"><![CDATA[
+        datamanager_create_reference.py 
+        --dbkey $genome.ensembl_genome_version 
+        --description "$genome.ensembl_prefix $genome.ensembl_genome_version ($genome.ucsc_genome_version)"
+        --defuse_config $defuse_config
+        --defuse_script $defuse_script
+        $out_file
+    ]]></command>
  <inputs>
   <conditional name="genome">
     <param name="choice" type="select" label="Select a Genome Build">
@@ -191,6 +191,7 @@
 fatotwobit_bin = __FATOTWOBIT_BIN__
 gmap_bin = __GMAP_BIN__
 gmap_setup_bin = __GMAP_SETUP_BIN__
+gmap_build_bin = __GMAP_BUILD_BIN__
 r_bin = __R_BIN__
 rscript_bin = __RSCRIPT_BIN__
 
@@ -246,29 +247,29 @@
 remove_job_temp_files                       = yes
 #end raw
   </configfile>
-  <configfile name="defuse_script">#slurp
+  <configfile name="defuse_script"><![CDATA[#slurp
 #!/bin/bash
 ## define some things for cheetah proccessing
-#set $amp = chr(38)
 #set $gt = chr(62)
 ## substitute pathnames into config file
-if `grep __DATASET_DIRECTORY__ $defuse_config ${gt} /dev/null`;then sed -i'.tmp' "s#__DATASET_DIRECTORY__#\$1#" $defuse_config; fi
-if `grep __DEFUSE_PATH__ $defuse_config ${gt} /dev/null`;then sed -i'.tmp' "s#__DEFUSE_PATH__#\${DEFUSE_PATH}#" $defuse_config; fi
-if `grep __SAMTOOLS_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} SAMTOOLS_BIN=`which samtools`;then sed -i'.tmp' "s#__SAMTOOLS_BIN__#\${SAMTOOLS_BIN}#" $defuse_config; fi
-if `grep __BOWTIE_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BOWTIE_BIN=`which bowtie`;then sed -i'.tmp' "s#__BOWTIE_BIN__#\${BOWTIE_BIN}#" $defuse_config; fi
-if `grep __BOWTIE_BUILD_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BOWTIE_BUILD_BIN=`which bowtie-build`;then sed -i'.tmp' "s#__BOWTIE_BUILD_BIN__#\${BOWTIE_BUILD_BIN}#" $defuse_config; fi
-if `grep __BLAT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BLAT_BIN=`which blat`;then sed -i'.tmp' "s#__BLAT_BIN__#\${BLAT_BIN}#" $defuse_config; fi
-if `grep __FATOTWOBIT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} FATOTWOBIT_BIN=`which faToTwoBit`;then sed -i'.tmp' "s#__FATOTWOBIT_BIN__#\${FATOTWOBIT_BIN}#" $defuse_config; fi
-if `grep __GMAP_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_BIN=`which gmap`;then sed -i'.tmp' "s#__GMAP_BIN__#\${GMAP_BIN}#" $defuse_config; fi
-if `grep __GMAP_SETUP_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_SETUP_BIN=`which gmap_setup`;then sed -i'.tmp' "s#__GMAP_SETUP_BIN__#\${GMAP_SETUP_BIN}#" $defuse_config; fi
-if `grep __GMAP_INDEX_DIR__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_INDEX_DIR=`pwd`/gmap;then sed -i'.tmp' "s#__GMAP_INDEX_DIR__#\${GMAP_INDEX_DIR}#" $defuse_config; fi
-if `grep __R_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} R_BIN=`which R`;then sed -i'.tmp' "s#__R_BIN__#\${R_BIN}#" $defuse_config; fi
-if `grep __RSCRIPT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} RSCRIPT_BIN=`which Rscript`;then sed -i'.tmp' "s#__RSCRIPT_BIN__#\${RSCRIPT_BIN}#" $defuse_config; fi
+export DATASET_DIRECTORY=$1
+if `grep __DATASET_DIRECTORY__ $defuse_config > /dev/null`;then sed -i'.tmp' "s#__DATASET_DIRECTORY__#\$DATASET_DIRECTORY#" $defuse_config; fi
+if `grep __DEFUSE_PATH__ $defuse_config > /dev/null`;then sed -i'.tmp' "s#__DEFUSE_PATH__#\${DEFUSE_PATH}#" $defuse_config; fi
+if `grep __SAMTOOLS_BIN__ $defuse_config > /dev/null` && SAMTOOLS_BIN=`which samtools`;then sed -i'.tmp' "s#__SAMTOOLS_BIN__#\${SAMTOOLS_BIN}#" $defuse_config; fi
+if `grep __BOWTIE_BIN__ $defuse_config > /dev/null` && BOWTIE_BIN=`which bowtie`;then sed -i'.tmp' "s#__BOWTIE_BIN__#\${BOWTIE_BIN}#" $defuse_config; fi
+if `grep __BOWTIE_BUILD_BIN__ $defuse_config > /dev/null` && BOWTIE_BUILD_BIN=`which bowtie-build`;then sed -i'.tmp' "s#__BOWTIE_BUILD_BIN__#\${BOWTIE_BUILD_BIN}#" $defuse_config; fi
+if `grep __BLAT_BIN__ $defuse_config > /dev/null` && BLAT_BIN=`which blat`;then sed -i'.tmp' "s#__BLAT_BIN__#\${BLAT_BIN}#" $defuse_config; fi
+if `grep __FATOTWOBIT_BIN__ $defuse_config > /dev/null` && FATOTWOBIT_BIN=`which faToTwoBit`;then sed -i'.tmp' "s#__FATOTWOBIT_BIN__#\${FATOTWOBIT_BIN}#" $defuse_config; fi
+if `grep __GMAP_BIN__ $defuse_config > /dev/null` && GMAP_BIN=`which gmap`;then sed -i'.tmp' "s#__GMAP_BIN__#\${GMAP_BIN}#" $defuse_config; fi
+if `grep __GMAP_BUILD_BIN__ $defuse_config > /dev/null` && GMAP_BUILD_BIN=`which gmap_setup`;then sed -i'.tmp' "s#__GMAP_BUILD_BIN__#\${GMAP_BUILD_BIN}#" $defuse_config; fi
+if `grep __GMAP_INDEX_DIR__ $defuse_config > /dev/null` && GMAP_INDEX_DIR=`pwd`/gmap;then sed -i'.tmp' "s#__GMAP_INDEX_DIR__#\${GMAP_INDEX_DIR}#" $defuse_config; fi
+if `grep __R_BIN__ $defuse_config > /dev/null` && R_BIN=`which R`;then sed -i'.tmp' "s#__R_BIN__#\${R_BIN}#" $defuse_config; fi
+if `grep __RSCRIPT_BIN__ $defuse_config > /dev/null` && RSCRIPT_BIN=`which Rscript`;then sed -i'.tmp' "s#__RSCRIPT_BIN__#\${RSCRIPT_BIN}#" $defuse_config; fi
 ## copy config to output
 cp $defuse_config \$1/defuse_config.txt
-## Run the create_reference_dataset.pl
-perl \${DEFUSE_PATH}/scripts/create_reference_dataset.pl -c $defuse_config 
-  </configfile>
+## Run defuse_create_ref.pl
+defuse_create_ref.pl --config $defuse_config --dataset $DATASET_DIRECTORY
+  ]]></configfile>
  </configfiles>
 
  <tests>