# HG changeset patch
# User galaxyp
# Date 1485787437 18000
# Node ID 2656b09d2046703d58dc5ea1567dca9fb4655680
# Parent  982fb2cde6c520235f7f5c9b88bee81a8e60f6c9
Uploaded

diff -r 982fb2cde6c5 -r 2656b09d2046 ._customProDB.xml
Binary file ._customProDB.xml has changed
diff -r 982fb2cde6c5 -r 2656b09d2046 customProDB.xml
--- a/customProDB.xml	Fri Jan 13 12:18:32 2017 -0500
+++ b/customProDB.xml	Mon Jan 30 09:43:57 2017 -0500
@@ -1,42 +1,46 @@
-<tool id="custom_pro_db" name="CustomProDB" version="1.10.0">
+<tool id="custom_pro_db" name="CustomProDB" version="1.14.0">
   <description>Generate protein FASTAs from exosome or transcriptome data</description>
+  <requirements>
+    <requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>
+  </requirements>
   <stdio>
     <exit_code range="1:" level="fatal" description="Job Failed" />
   </stdio>
-  <command interpreter="Rscript --vanilla">customProDB.R
-
-       --bam="$genome_annotation.bamInput"
-       --bai="${genome_annotation.bamInput.metadata.bam_index}"
-       --vcf="$genome_annotation.vcfInput"
+  <command><![CDATA[
+    Rscript --vanilla '$__tool_directory__/customProDB.R'
+       --bam='$genome_annotation.bamInput'
+       --bai='${genome_annotation.bamInput.metadata.bam_index}'
+       --vcf='$genome_annotation.vcfInput'
        --rpkmCutoff=$rpkmCutoff
-       --outputFile="${output_rpkm}"
+       --outputFile='${output_rpkm}'
 
-       #if str($genome_annotation.source) == "history":
-            --exon_anno="$genome_annotation.exonAnno"
-            --proteinseq="$genome_annotation.proteinSeq"
-            --procodingseq="$genome_annotation.proCodingSeq"
-            --ids="$genome_annotation.ids"
-            #if str($genome_annotation.dbsnpInCoding) != "None":
-                --dbsnpinCoding="$genome_annotation.dbsnpInCoding"
+       #if str($genome_annotation.source) == 'history':
+            --exon_anno='$genome_annotation.exonAnno'
+            --proteinseq='$genome_annotation.proteinSeq'
+            --procodingseq='$genome_annotation.proCodingSeq'
+            --ids='$genome_annotation.ids'
+            #if str($genome_annotation.dbsnpInCoding) != 'None':
+                --dbsnpinCoding='$genome_annotation.dbsnpInCoding'
             #end if
-            #if str($genome_annotation.cosmic) != "None":
-                --cosmic="$genome_annotation.cosmic"
+            #if str($genome_annotation.cosmic) != 'None':
+                --cosmic='$genome_annotation.cosmic"
             #end if
        #else:
             #set index_path = $genome_annotation.builtin.fields.path
-            --exon_anno="$index_path/exon_anno.RData"
-            --proteinseq="$index_path/proseq.RData"
-            --procodingseq="$index_path/procodingseq.RData"
-            --ids="$index_path/ids.RData"
+            --exon_anno='$index_path/exon_anno.RData'
+            --proteinseq='$index_path/proseq.RData'
+            --procodingseq='$index_path/procodingseq.RData'
+            --ids='$index_path/ids.RData'
             #if $genome_annotation.dbsnpInCoding:
-                --dbsnpinCoding="$index_path/dbsnpinCoding.RData"
+                --dbsnpinCoding='$index_path/dbsnpinCoding.RData'
             #end if
             #if $genome_annotation.cosmic:
-                --cosmic="$index_path/cosmic.RData"
+                --cosmic='$index_path/cosmic.RData'
             #end if
        #end if
-
-2&gt;&amp;1</command>
+       2>1
+]]>
+  </command>
   <inputs>
     <conditional name="genome_annotation">
       <param name="source" type="select" label="Will you select a genome annotation from your history or use a built-in annotation?" help="See `Annotations` section of help below">
@@ -73,9 +77,9 @@
         <param name="bamInput" type="data" format="bam" label="BAM file">
             <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
         </param>
-        <param name="baiInput" type="data" format="bam_index" label="BAM Index file">
+        <!--<param name="baiInput" type="data" format="bam_index" label="BAM Index file">
             <validator check="dbkey" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
-        </param>
+        </param>-->
         <param name="vcfInput" type="data" format="vcf" label="VCF file" />
         <param name="dbsnpInCoding" type="data" format="RData" label="A dataframe containing dbSNP rsids" optional="true" />
         <param name="cosmic" type="data" format="RData" label="A dataframe containing somatic SNPs from COSMIC (human only)" optional="true" />
@@ -102,10 +106,12 @@
       <output name="output_indel" file="test_indel.fasta" />
     </test>
   </tests>
-  <help>
+  <help><![CDATA[
 **Description**
 
-Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files). </help>
+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