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changeset 1:d16cc2d33359 draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:35:51 -0400
parents f64b81fda062
children ced02f5334a0
files rgWebLogo3.xml tool_dependencies.xml
diffstat 2 files changed, 11 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/rgWebLogo3.xml	Thu Jan 23 12:30:59 2014 -0500
+++ b/rgWebLogo3.xml	Tue Oct 13 12:35:51 2015 -0400
@@ -1,6 +1,7 @@
 <tool id="rgweblogo3" name="Sequence Logo" version="0.4">
    <description>generator for fasta (eg Clustal alignments)</description>
    <requirements>
+      <requirement type="package" version="1.7.1">numpy</requirement>
       <requirement type="package" version="3.3">weblogo</requirement>
       <requirement type="package" version="9.10">ghostscript</requirement>
    </requirements>
@@ -13,14 +14,14 @@
   <inputs>
    <page>
     <param format="fasta" name="input" type="data" label="Fasta File" />
-    <param name="logoname" label="Title for output Sequence Logo" type="text" size="50" value="Galaxy-Rgenetics Sequence Logo" />
+    <param name="logoname" label="Title for output Sequence Logo" type="text" value="Galaxy-Rgenetics Sequence Logo" />
     <param name="outformat" type="select" label="Output format for image (or text report)" >
       <option value="png" selected="True">PNG screen quality</option>
       <option value="png_print">High quality printable PNG</option>
       <option value="pdf">PDF</option>
       <option value="jpeg">JPG</option>
       <option value="eps">EPS</option>
-      <option value="txt">Text (shows the detailed calculations for each position - no image)</option>
+      <option value="logodata">Text (shows the detailed calculations for each position - no image)</option>
     </param>
     <param name="units" type="select" label="Display Units"
       help="What the height of each logo element depicts - eg bits of entropy (default)">
@@ -51,10 +52,10 @@
         <when value="complete">
         </when>
         <when value="part">    
-           <param name="seqstart" size="5" type="integer" value="1" help="WARNING: Specifying indexes outside the sequence lengths will cause unpredictable but bad consequences!" 
+           <param name="seqstart" type="integer" value="1" help="WARNING: Specifying indexes outside the sequence lengths will cause unpredictable but bad consequences!" 
              label="Index (eg 1=first letter) of the start of the sequence range to include in the logo">
            </param>
-           <param name="seqend" size="5" type="integer" value="99999" label="Index (eg 75=75th letter) of the end of the sequence range to include in the logo" >
+           <param name="seqend" type="integer" value="99999" label="Index (eg 75=75th letter) of the end of the sequence range to include in the logo" >
            </param> 
         </when>
     </conditional>
@@ -72,7 +73,7 @@
            <when input="outformat" value="png" format="png" />
            <when input="outformat" value="jpeg" format="jpg" />
            <when input="outformat" value="eps" format="eps" />
-           <when input="outformat" value="txt" format="txt" />
+           <when input="outformat" value="logodata" format="txt" />
        </change_format>
     </data>
   </outputs>
--- a/tool_dependencies.xml	Thu Jan 23 12:30:59 2014 -0500
+++ b/tool_dependencies.xml	Tue Oct 13 12:35:51 2015 -0400
@@ -1,9 +1,12 @@
 <?xml version="1.0"?>
 <tool_dependency>
   <package name="ghostscript" version="9.10">
-      <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="False" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="numpy" version="1.7.1">
+        <repository changeset_revision="5c489d2d630b" name="package_numpy_1_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="weblogo" version="3.3">
-      <repository changeset_revision="18cb94906560" name="package_weblogo_3_3" owner="devteam" prior_installation_required="False" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="18cb94906560" name="package_weblogo_3_3" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>