# HG changeset patch
# User galaxyp
# Date 1481845281 18000
# Node ID 6bbce76c78c12926c8285c81d9b7277e0b17a734
# Parent  d723eb657f1d04032893465176b093caefb9109c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 7025b29e8113049e5f21389ce67858c18af6611b

diff -r d723eb657f1d -r 6bbce76c78c1 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Jan 25 12:21:21 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="biopython" version="1.62">
-        <repository changeset_revision="f06c96348778" name="package_biopython_1_62" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>
diff -r d723eb657f1d -r 6bbce76c78c1 translate_bed_sequences.xml
--- a/translate_bed_sequences.xml	Mon Jan 25 12:21:21 2016 -0500
+++ b/translate_bed_sequences.xml	Thu Dec 15 18:41:21 2016 -0500
@@ -1,121 +1,118 @@
-<?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 ${on_string} fasta">
-    </data>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input" value="Extract_Genomic_DNA.bed" ftype="bed" dbkey="hg19"/>
-      <param name="reference" value="GRCh37"/>
-      <param name="seqtype" value="pep:novel"/>
-      <param name="score_name" value="depth"/>
-      <output name="output" file="translated_bed_sequences.fa"/>
-    </test>
-  </tests>
-  <help>
+<tool id="translate_bed_sequences" name="Translate BED Sequences" version="0.1.1">
+    <description>3 frame translation of BED augmented with a sequence column</description>
+    <requirements>
+        <requirement type="package" version="1.62">biopython</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Error" />
+    </stdio>
+    <command>
+    python '$__tool_directory__/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>
+    <outputs>
+        <data name="translated_bed" metadata_source="input" format="bed" label="${tool.name} on ${on_string} bed" />
+        <data name="output" metadata_source="input" format="fasta" label="${tool.name} on ${on_string} fasta" />
+    </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 
@@ -124,5 +121,5 @@
 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>
+    </help>
 </tool>