--- a/customProDB.xml	Tue Mar 14 14:14:38 2017 -0400
+++ b/customProDB.xml	Fri May 12 13:17:40 2017 -0400
@@ -1,8 +1,24 @@
-<tool id="custom_pro_db" name="CustomProDB" version="1.14.0">
+<tool id="custom_pro_db" name="CustomProDB" version="1.16.0">
   <description>Generate protein FASTAs from exosome or transcriptome data</description>
   <requirements>
-    <requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>
+    <requirement type="package" version="3.3.1">r-base</requirement>
+    <!--<requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>-->
     <requirement type="package" version="1.18.0">bioconductor-rgalaxy</requirement>
+    <requirement type="package" version="1.21.0">bioconductor-biocinstaller</requirement>
+    <requirement type="package" version="1.20.3">bioconductor-variantannotation</requirement>
+    <requirement type="package" version="1.11.1">r-devtools</requirement>
+    <requirement type="package" version="3.98_1.4">r-xml</requirement>
+    <requirement type="package" version="0.10.11">r-rmysql</requirement>
+    <requirement type="package" version="1.0.2">r-testthat</requirement>
+    <requirement type="package" version="0.1.0">r-getoptlong</requirement>
+    <requirement type="package" version="1.1.2">r-stringi</requirement>
+    <requirement type="package" version="1.1.0">r-stringr</requirement>
+    <requirement type="package" version="1.10.0">r-data.table</requirement>
+    <!--<requirement type="package" version="0.4_10">r-sqldf</requirement>-->
+    <requirement type="package" version="0.6_6">r-gsubfn</requirement>
+    <requirement type="package" version="2.3_47">r-chron</requirement>
+    <requirement type="package" version="0.3.10">r-proto</requirement>
+    <requirement type="package" version="1.8.4">r-plyr</requirement>
   </requirements>
   <stdio>
     <exit_code range="1:" level="fatal" description="Job Failed" />
@@ -13,7 +29,9 @@
        --bai='${genome_annotation.bamInput.metadata.bam_index}'
        --vcf='$genome_annotation.vcfInput'
        --rpkmCutoff=$rpkmCutoff
-       --outputFile='${output_rpkm}'
+       $outputIndels
+       $outputSQLite
+       $outputRData
 
        #if str($genome_annotation.source) == 'history':
             --exon_anno='$genome_annotation.exonAnno'
@@ -24,7 +42,7 @@
                 --dbsnpinCoding='$genome_annotation.dbsnpInCoding'
             #end if
             #if str($genome_annotation.cosmic) != 'None':
-                --cosmic='$genome_annotation.cosmic"
+                --cosmic='$genome_annotation.cosmic'
             #end if
        #else:
             #set index_path = $genome_annotation.builtin.fields.path
@@ -87,24 +105,77 @@
       </when>
     </conditional>
     <param name="rpkmCutoff" type="float" value="1" min="0" label="Transcript Expression Cutoff (RPKM)" help="If non-zero, if a transcript does not meet this expression cutoff (based on RPKM) then it will not be included in the output database." />
+    <param name="outputIndels" type="boolean" truevalue="--outputIndels" falsevalue="" label="Create a variant FASTA for short insertions and deletions" />
+    <param name="outputSQLite" type="boolean" truevalue="--outputSQLite" falsevalue="" label="Create SQLite files for mapping proteins to genome and summarizing variant proteins" />
+    <param name="outputRData" type="boolean" truevalue="--outputRData" falsevalue="" label="Create RData file of variant protein coding sequences" help="The PSM2SAM tool needs this to map variant proteins to genomic locations" />
   </inputs>
   <outputs>
     <data format="fasta" name="output_rpkm" from_work_dir="output_rpkm.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_rpkm.fasta"/>
     <data format="fasta" name="output_snv" from_work_dir="output_snv.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_snv.fasta"/>
-    <data format="fasta" name="output_indel" from_work_dir="output_indel.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_indel.fasta"/>
+    <data format="fasta" name="output_indel" from_work_dir="output_indel.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_indel.fasta">
+      <filter>outputIndels is True</filter>
+    </data>
+    <data format="rdata" name="output_variant_annotation_rdata" from_work_dir="output.rdata" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_variantAnnotation.RData">
+      <filter>outputRData is True</filter>
+    </data>
+    <data format="sqlite" name="output_genomic_mapping_sqlite" from_work_dir="output_genomic_mapping.sqlite" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_genomicMapping.sqlite">
+      <filter>outputSQLite is True</filter>
+    </data>
+    <data format="sqlite" name="output_variant_annotation_sqlite" from_work_dir="output_variant_annotation.sqlite" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_variantAnnotation.sqlite">
+      <filter>outputSQLite is True</filter>
+    </data>
   </outputs>
   <tests>
-    <test>
-      <param name="bamInput" value="test1_sort.bam" dbkey="hg19" />
-      <param name="vcfInput" value="test1.vcf" dbkey="hg19" />
+    <test expect_num_outputs="5">
+      <param name="bamInput" value="hg19/test1_sort.bam" dbkey="hg19" />
+      <param name="vcfInput" value="hg19/test1.vcf" dbkey="hg19" />
+      <param name="source" value="history" />
+      <param name="exonAnno" value="hg19/exon_anno.RData" />
+      <param name="proteinSeq" value="hg19/proseq.RData" />
+      <param name="proCodingSeq" value="hg19/procodingseq.RData" />
+      <param name="ids" value="hg19/ids.RData" />
+      <param name="rpkmCutoff" value="1" />
+      <param name="outputIndels" value="" />
+      <param name="outputRData" value="--outputRData" />
+      <param name="outputSQLite" value="--outputSQLite" />
+      <output name="output_rpkm" file="hg19_rpkm1.fasta" />
+      <output name="output_snv" file="hg19_snv.fasta" />
+      <output name="output_variant_annotation_rdata" file="hg19_variant_annotation.rdata" />
+      <output name="output_genomic_mapping_sqlite" file="hg19_genomic_mapping.sqlite" />
+      <output name="output_variant_annotation_sqlite" file="hg19_variant_annotation.sqlite" />
+    </test>
+    <test expect_num_outputs="5">
+      <param name="bamInput" value="hg19/test1_sort.bam" dbkey="hg19" />
+      <param name="vcfInput" value="hg19/test1.vcf" dbkey="hg19" />
       <param name="source" value="history" />
-      <param name="exonAnno" value="exon_anno.RData" />
-      <param name="proteinSeq" value="proseq.RData" />
-      <param name="proCodingSeq" value="procodingseq.RData" />
-      <param name="ids" value="ids.RData" />
-      <output name="output_rpkm" file="test_rpkm.fasta" />
-      <output name="output_snv" file="test_snv.fasta" />
-      <output name="output_indel" file="test_indel.fasta" />
+      <param name="exonAnno" value="hg19/exon_anno.RData" />
+      <param name="proteinSeq" value="hg19/proseq.RData" />
+      <param name="proCodingSeq" value="hg19/procodingseq.RData" />
+      <param name="ids" value="hg19/ids.RData" />
+      <param name="dbsnpInCoding" value="hg19/dbsnpinCoding.RData" />
+      <param name="cosmic" value="hg19/cosmic.RData" />
+      <param name="rpkmCutoff" value="0" />
+      <param name="outputIndels" value="--outputIndels" />
+      <param name="outputSQLite" value="--outputSQLite" />
+      <output name="output_rpkm" file="hg19_rpkm0.fasta" />
+      <output name="output_snv" file="hg19_dbsnp_snv.fasta" />
+      <output name="output_indel" file="hg19_indel.fasta" />
+      <output name="output_variant_annotation_rdata" file="hg19_dbsnp_variant_annotation.rdata" />
+      <output name="output_variant_annotation_sqlite" file="hg19_dbsnp_variant_annotation.sqlite" />
+    </test>
+    <test expect_num_outputs="3">
+      <param name="bamInput" value="hg19/test1_sort.bam" dbkey="hg19" />
+      <param name="vcfInput" value="hg19/test1.vcf" dbkey="hg19" />
+      <param name="source" value="history" />
+      <param name="exonAnno" value="hg19/exon_anno.RData" />
+      <param name="proteinSeq" value="hg19/proseq.RData" />
+      <param name="proCodingSeq" value="hg19/procodingseq.RData" />
+      <param name="ids" value="hg19/ids.RData" />
+      <param name="rpkmCutoff" value="1000" />
+      <param name="outputIndels" value="--outputIndels" />
+      <output name="output_rpkm" file="hg19_rpkm1000.fasta" />
+      <output name="output_snv" file="hg19_snv.fasta" />
+      <output name="output_indel" file="hg19_indel.fasta" />
     </test>
   </tests>
   <help>
@@ -113,8 +184,7 @@
 Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files). </help>
   <citations>
     <citation type="doi">10.1093/bioinformatics/btt543</citation>
-    <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub 
-repository},
+    <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
                                   year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = 
 {$sha1$}" -->
   </citations>