diff translate_bed_sequences.xml @ 5:c626a939eef7 draft default tip

Uploaded

--- a/translate_bed_sequences.xml	Thu Jan 30 13:26:58 2014 -0600
+++ b/translate_bed_sequences.xml	Tue Jan 12 14:38:03 2016 -0500
@@ -1,16 +1,29 @@
 <?xml version="1.0"?>
-<tool id="translate_bed_sequences" name="Translate BED Sequences" version="0.0.1">
+<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 "$input" 
+  <command interpreter="python">
+  translate_bed_sequences.py  --input "$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
@@ -29,18 +42,31 @@
   #end if
   #if $trim.trimseqs == 'no':
     --untrimmed
-    #if $trim.max_stop_codons.__str__ != '':
+    #if str($trim.max_stop_codons) != '':
       --max_stop_codons $trim.max_stop_codons
     #end if
   #end if
-  #if $min_length:
+  #if str($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 source, e.g. generic"
+           help="Only used when a fasta ID source is given, default 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_-|]*$</validator>
+    </param>
+    <param name="refsource" type="text" value="Ensembl" optional="true" label="Genome reference source"
+           help=""/>
     <param name="reference" type="text" value="" optional="true" label="Genome reference name"
            help="By default, the database metadata will be used."/>
     <param name="seqtype" type="text" value="" optional="true" label="The SEQTYPE:STATUS to include in the fasta ID lines"
@@ -75,8 +101,9 @@
     <exit_code range="1:" level="fatal" description="Error" />
   </stdio>
   <outputs>
-    <data name="output" metadata_source="input" format="fasta" label="${tool.name} on ${on_string}">
-      <filter>'found' in str(outputs)</filter>
+    <data name="translated_bed" metadata_source="input" format="bed" label="${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>
@@ -97,6 +124,5 @@
 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>
 </tool>