Mercurial > repos > iracooke > sixframe_translate

diff sixframe_translate.xml @ 2:e20c4df2bc28 draft default tip

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/sixframe-translate/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:40:02 -0400
parents 10465e20d9a2
children
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--- a/sixframe_translate.xml	Thu Mar 26 19:56:34 2015 -0400
+++ b/sixframe_translate.xml	Tue Oct 20 20:40:02 2015 -0400
@@ -1,55 +1,55 @@
-<tool id="sixframe_translate" name="Generate 6-frame translation" version="1.1.0">
-	<requirements>
-        <container type="docker">iracooke/protk-1.4.1</container>		
-	    <requirement type="package" version="1.4">protk</requirement>
-   </requirements>
-
-	<description>Translates DNA/RNA to protein</description>
-
-	<command>
-		sixframe.rb $fasta_file -o $output $strip_header $coords
-	</command>
-
-
-
-
-	<stdio>
-		<exit_code range="1:"   level="fatal"   description="Failure" />
-	</stdio>
+<tool id="sixframe_translate" name="Generate 6-frame translation" version="1.1.1">
+    <description>Translates DNA/RNA to protein</description>
+    <requirements>
+        <container type="docker">iracooke/protk-1.4.3</container>
+        <requirement type="package" version="1.4.3">protk</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Failure" />
+    </stdio>
+    <command>
+        sixframe.rb
+        $fasta_file
+        -o $output
+        $strip_header
+        $coords
+        $peptideshaker
+        --min-len $minlen
 
-	<inputs>	
-		<param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
-		<param name="strip_header" type="boolean" label="Strip header info" help="" truevalue="--strip-header" falsevalue="" />
-		<param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--coords" falsevalue="" />
-	</inputs>
-
-	<outputs>
-		<data format="fasta" name="output" />
-	</outputs>
-
-	<tests>
-	  <test>
-	      <param name="fasta_file" value="small_genome.fasta" format="fasta"/>
-	      <output name="output" format="fasta">
-	          <assert_contents>
-	              <has_text text="SVQHWFYRFQAGHPRVFCPKNGPRRLW" />
-	          </assert_contents>
-	      </output>
-	  </test>
-	</tests>
-
-
-  <help>
+        #if $gffoutput:
+            --gff
+        #end if
+    </command>
+    <inputs>
+        <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
+        <param name="strip_header" type="boolean" label="Strip header info" help="" truevalue="--strip-header" falsevalue="" />
+        <param name="gffoutput" type="boolean" label="Produce gff instead of fasta" help="" truevalue="true" falsevalue="false" />
+        <param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--coords" falsevalue="" />
+        <param name="peptideshaker" type="boolean" label="Format fasta entries for PeptideShaker" help="" truevalue="--peptideshaker" falsevalue="" />
+        <param name="minlen" type="integer" value="20" min="1" label="Minimum Peptide Length"/>
+    </inputs>
+    <outputs>
+        <data format="fasta" name="output">
+            <change_format>
+                <when input="gffoutput" value="true" format="gff3" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+      <test>
+          <param name="fasta_file" value="small_genome.fasta" format="fasta"/>
+          <output name="output" format="fasta">
+              <assert_contents>
+                  <has_text text="SVQHWFYRFQAGHPRVFCPKNGPRRLW" />
+              </assert_contents>
+          </output>
+      </test>
+    </tests>
+    <help>
 
 **What it does**
 
 Generates 6 frame translations suitable for proteogenomics workflows
 
-----
-
-**References**
-
-
-  </help>
-
+    </help>
 </tool>