--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/translate_bed_sequences.xml	Mon Jan 25 12:21:21 2016 -0500
@@ -0,0 +1,128 @@
+<?xml version="1.0"?>
+<tool id="translate_bed_sequences" name="Translate BED Sequences" version="0.1.0">
+  <description>3 frame translation of BED augmented with a sequence column</description>
+  <requirements>
+    <requirement type="package" version="1.62">biopython</requirement>
+    <requirement type="python-module">Bio</requirement>
+  </requirements>
+  <command interpreter="python">
+  translate_bed_sequences.py  --input "$input" 
+  #if $fa_db:
+   --fa_db='$fa_db'
+  #end if
+  #if $fa_sep:
+   --fa_sep='$fa_sep'
+  #end if
+  #if $id_prefix:
+   --id_prefix='$id_prefix'
+  #end if
+  #if $reference:
+   --reference $reference
+  #else:
+   --reference ${input.metadata.dbkey}
+  #end if
+  #if $refsource:
+   --refsource $refsource
+  #end if
+  #if $seqtype:
+    --seqtype $seqtype
+  #end if
+  #if $score_name:
+    --score_name $score_name
+  #end if
+  #if $filter.filterseqs == 'yes':
+    #if $filter.leading_bp:
+      --leading_bp $filter.leading_bp
+    #end if
+    #if $filter.trailing_bp:
+      --trailing_bp $filter.trailing_bp
+    #end if
+  #else:
+    --unfiltered
+  #end if
+  #if $trim.trimseqs == 'no':
+    --untrimmed
+    #if str($trim.max_stop_codons) != '':
+      --max_stop_codons $trim.max_stop_codons
+    #end if
+  #end if
+  #if str($min_length) != '':
+   --min_length $min_length 
+  #end if
+  --bed $translated_bed
+  --output "$output"
+  </command>
+  <inputs>
+    <param name="input" type="data" format="bed" label="BED file with added sequence column" 
+           help="Output from 'Extract Genomic DNA' run on tophat junctions.bed "/> 
+    <param name="fa_db" type="text" value="" optional="true" label="fasta ID source, e.g. generic"
+           help="Any Compomics application such as PeptideShaker, requires a source">
+    </param>
+    <param name="fa_sep" type="text" value="" optional="true" label="fasta ID line separator character"
+           help="Only used when a fasta ID source is given, defaults to the pipe character">
+    </param>
+    <param name="id_prefix" type="text" value="" optional="true" label="ID prefix for generated IDs"
+           help="Can be used to distinguish samples">
+        <validator type="regex" message="Allowed chars:a-z A-Z 0-9 _ - |">^[a-zA-Z0-9_-|]*$</validator>
+    </param>
+    <param name="refsource" type="text" value="Ensembl" optional="true" label="Genome reference source"
+           help=""/>
+    <param name="reference" type="text" value="" optional="true" label="Genome reference name"
+           help="By default, the database metadata will be used."/>
+    <param name="seqtype" type="text" value="" optional="true" label="The SEQTYPE:STATUS to include in the fasta ID lines"
+           help="For example:  pep:splice"/>
+    <param name="score_name" type="text" value="" optional="true" label="Add the bed score field fasta ID line with this tag name"
+           help="For example:  with the tag name 'depth' and bed score 12:   depth:12"/>
+    <conditional name="filter">
+      <param name="filterseqs" type="select" label="Filter out translations with stop codons before the splice site">
+        <option value="yes" selected="true">Yes</option>
+        <option value="no">No</option>
+      </param>
+      <when value="yes">
+        <param name="leading_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering start position base pairs" 
+               help="Do not reject translation is stop_codons are within base pairs of the BED start position for positive strand"/>
+        <param name="trailing_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering end position base pairs" 
+               help="Do not reject translation is stop_codons are within base pairs of the BED end position for negative strand"/>
+      </when>
+      <when value="no"/>
+    </conditional>
+    <conditional name="trim">
+      <param name="trimseqs" type="select" label="Trim translations to stop codons">
+        <option value="yes" selected="true">Yes</option>
+        <option value="no">No</option>
+      </param>
+      <when value="no">
+        <param name="max_stop_codons" type="integer" value="" min="0" optional="true" label="Maximum number of stop codons allowed in a translation to be reported"/>
+      </when>
+    </conditional>
+    <param name="min_length" type="integer" value="" min="0" optional="true" label="Minimum length of a translation to be reported"/>
+  </inputs>
+  <stdio>
+    <exit_code range="1:" level="fatal" description="Error" />
+  </stdio>
+  <outputs>
+    <data name="translated_bed" metadata_source="input" format="bed" label="${tool.name} on ${on_string} bed">
+    </data>
+    <data name="output" metadata_source="input" format="fasta" label="${tool.name} on ${on_string} fasta">
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="Extract_Genomic_DNA.bed" ftype="bed" dbkey="hg19"/>
+      <param name="reference" value="GRCh37"/>
+      <param name="seqtype" value="pep:novel"/>
+      <param name="score_name" value="depth"/>
+      <output name="output" file="translated_bed_sequences.fa"/>
+    </test>
+  </tests>
+  <help>
+**Translate BED Sequences**
+
+This tool takes a BED input file that has been processed 
+by the Galaxy tool "Extract Genomic DNA" to add a 13th column with the transcript sequence.
+
+It generates a peptide fasta file with the 3-frame translations of the spliced sequence 
+defined by each entry in the input BED file.
+
+  </help>
+</tool>