diff emboss_sixpack.xml @ 14:27c43fb015f0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
author iuc
date Fri, 22 Jun 2018 03:24:29 -0400
parents 0e2484b6829b
children 21a9fb508031
line wrap: on
line diff
--- a/emboss_sixpack.xml	Mon Apr 23 13:04:47 2018 -0400
+++ b/emboss_sixpack.xml	Fri Jun 22 03:24:29 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="EMBOSS: sixpack90" name="sixpack" version="5.0.0.1">
+<tool id="EMBOSS: sixpack90" name="sixpack" version="@VERSION@+galaxy2">
   <!-- tool adds file description and timestamp to output data -->
   <description>Display a DNA sequence with 6-frame translation and ORFs</description>
   <macros>
@@ -6,8 +6,12 @@
   </macros>
   <expand macro="requirements" />
   <code file="emboss_format_corrector.py" />
-  <command>sixpack -sequence '$input1' -outfile '$ofile1' -outseq '$ofile2' -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize -uppercase
-  '$uppercase' -number $number -width $width -length $length -margin $margin -name $disp_name -description $description -offset $offset -html $html_out1 -osformat $out_format2 -auto</command>
+  <command><![CDATA[
+    sixpack -sequence '$input1' -outfile '$ofile1' -outseq '$ofile2' -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize 
+    #if str($uppercase):
+      -uppercase '$uppercase' 
+    #end if  
+    -number $number -width $width -length $length -margin $margin -name $disp_name -description $description -offset $offset -html $html_out1 -osformat $out_format2 -auto]]></command>
   <inputs>
     <param name="input1" type="data" format="fasta" label="Sequences" />
     <param name="table" type="select" label="Code to use">
@@ -47,7 +51,7 @@
       <option value="no">No</option>
     </param>
     <param name="orfminsize" type="integer" value="1" label="Minimum size of Open Reading Frames (ORFs) to display in the translations" />
-    <param name="uppercase" type="text" value="" label="Regions to put in uppercase" />
+    <param name="uppercase" type="text" value="" label="Regions to put in uppercase" help="If this is left blank, then the sequence case is left alone. A set of regions is specified by a set of pairs of positions. The positions are integers. They are separated by any non-alpha-numeric character. Three examples of region specifications are: 1) 24-45, 56-78 2) 1:45, 67=99;765..888 3) 1,5,8,10,23,45,57,99"/>
     <param name="number" type="select" label="Number the sequence at the beginning and the end of each line">
       <option value="yes">Yes</option>
       <option value="no">No</option>
@@ -104,7 +108,7 @@
     <data name="ofile1" format="sixpack" />
     <data name="ofile2" format="fasta" />
   </outputs>
-<!--    <tests>
+  <tests>
     <test>
       <param name="input1" value="2.fasta"/>
       <param name="table" value="0"/>
@@ -123,9 +127,10 @@
       <param name="offset" value="1"/>
       <param name="html_out1" value="no"/>
       <param name="out_format2" value="fasta"/>
+      <output name="ofile1" file="emboss_sixpack_out2.sixpack" />
       <output name="ofile2" file="emboss_sixpack_out.fasta"/>
     </test>
-  </tests> -->
+  </tests>
   <help>
 .. class:: warningmark