diff galaxyp-toolshed-proteinpilot @ 2:ebeaa403d9eb

improved some datatype handling
author galaxyp
date Thu, 20 Jun 2013 10:50:41 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxyp-toolshed-proteinpilot	Thu Jun 20 10:50:41 2013 -0400
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+              </a>
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+                
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+              
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+  
+    
+    
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+        
+          
+<section class="bb-banner" id="signup-banner">
+  <div>
+    <p>
+      
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+    <span class="close aui-icon aui-icon-small aui-iconfont-close-dialog" title="Dismiss this banner">Close</span>
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+</section>
+
+        
+        
+          
+            
+              <section id="readme">
+                
+                  <article class="readme file">
+                    <p>TODO: Document this tool repository.</p>
+<h1 id="markdown-header-obtaining-tools">Obtaining Tools</h1>
+<p>Repositories for all Galaxy-P tools can be found at
+https:/bitbucket.org/galaxyp/.</p>
+<h1 id="markdown-header-contact">Contact</h1>
+<p>Please send suggestions for improvements and bug reports to
+jmchilton@gmail.com.</p>
+<h1 id="markdown-header-license">License</h1>
+<p>All Galaxy-P tools are licensed under the Apache License Version 2.0
+unless otherwise documented.</p>
+<h1 id="markdown-header-tool-versioning">Tool Versioning</h1>
+<p>Galaxy-P tools will have versions of the form X.Y.Z. Versions
+differing only after the second decimal should be completely
+compatible with each other. Breaking changes should result in an
+increment of the number before and/or after the first decimal. All
+tools of version less than 1.0.0 should be considered beta.</p>
+                  </article>
+                
+              </section>
+            
+          
+        
+        <section id="repo-activity">
+          <h1>
+            Recent activity
+            <a href="/galaxyp/galaxyp-toolshed-proteinpilot/rss" class="icon rss">RSS feed fo galaxyp-toolshed-proteinpilot</a>
+          </h1>
+          
+            
+              
+                
+
+
+   
+
+
+<div class="newsfeed">
+  
+    
+      
+        
+          
+            
+            
+            
+              
+                
+            
+              <article class="news-item commit">
+                <span class="icon commit"></span>
+                
+
+
+  <a href="/galaxyp"><img alt="galaxyp" src="https://secure.gravatar.com/avatar/655358b258b3fbd64aa5c6f42adade4e?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_team_avatar%2F32%2Fteam_blue.png&amp;s=32" class="avatar avatar32" /></a>
+
+
+                <p>
+                  
+
+  <a href="/galaxyp">galaxyp</a>
+
+                  pushed 1 commit to 
+
+
+<a href="/galaxyp/galaxyp-toolshed-proteinpilot" title="galaxyp/galaxyp-toolshed-proteinpilot">galaxyp/galaxyp-toolshed-proteinpilot</a>
+
+
+                </p>
+                <time datetime="2013-06-20T14:34:36+00:00">16 minutes ago</time>
+                
+                  <div class="changeset">
+                  <a href="/galaxyp/galaxyp-toolshed-proteinpilot/commits/478c9dfebeb1844401c1f5fcf6a55fefa6796655" class="changeset-hash">478c9df</a>
+                  -
+                  
+                    
+                      improved some datatype handling
+                    
+                  
+                  </div>
+                
+                
+              </article>
+            
+
+              
+            
+          
+          
+        
+      
+    
+  
+    
+      
+        
+          
+            
+              </article>
+            
+            
+            
+              
+                
+            
+              <article class="news-item commit">
+                <span class="icon commit"></span>
+                
+
+
+  <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&amp;s=32" class="avatar avatar32" /></a>
+
+
+                <p>
+                  
+
+  <a href="/jmchilton">John Chilton</a>
+
+                  pushed 1 commit to 
+
+
+<a href="/galaxyp/galaxyp-toolshed-proteinpilot" title="galaxyp/galaxyp-toolshed-proteinpilot">galaxyp/galaxyp-toolshed-proteinpilot</a>
+
+
+                </p>
+                <time datetime="2013-05-05T19:06:30+00:00">2013-05-05</time>
+                
+                  <div class="changeset">
+                  <a href="/galaxyp/galaxyp-toolshed-proteinpilot/commits/eeb0664db8240d23a79fc406b6ae7c39f8159291" class="changeset-hash">eeb0664</a>
+                  -
+                  
+                    
+                      Add TMT options to protein pilot.
+                    
+                  
+                  </div>
+                
+                
+              </article>
+            
+
+              
+            
+          
+          
+        
+      
+    
+  
+    
+      
+        
+          
+            
+              
+                
+            
+              <article class="news-item commit">
+                <span class="icon commit"></span>
+                
+
+
+  <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&amp;s=32" class="avatar avatar32" /></a>
+
+
+                <p>
+                  
+
+  <a href="/jmchilton">John Chilton</a>
+
+                  pushed 1 commit to 
+
+
+<a href="/galaxyp/galaxyp-toolshed-proteinpilot" title="galaxyp/galaxyp-toolshed-proteinpilot">galaxyp/galaxyp-toolshed-proteinpilot</a>
+
+
+                </p>
+                <time datetime="2013-04-22T15:57:02+00:00">2013-04-22</time>
+                
+                  <div class="changeset">
+                  <a href="/galaxyp/galaxyp-toolshed-proteinpilot/commits/3d9ab1d73205383c046a753bf779f707ae616d57" class="changeset-hash">3d9ab1d</a>
+                  -
+                  
+                    
+                      Fix name versus display_name property access.
+                    
+                  
+                  </div>
+                
+                
+              </article>
+            
+
+              
+            
+          
+          
+        
+      
+    
+  
+    
+      
+        
+          
+            
+              
+                
+            
+              <article class="news-item commit">
+                <span class="icon commit"></span>
+                
+
+
+  <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&amp;s=32" class="avatar avatar32" /></a>
+
+
+                <p>
+                  
+
+  <a href="/jmchilton">John Chilton</a>
+
+                  pushed 1 commit to 
+
+
+<a href="/galaxyp/galaxyp-toolshed-proteinpilot" title="galaxyp/galaxyp-toolshed-proteinpilot">galaxyp/galaxyp-toolshed-proteinpilot</a>
+
+
+                </p>
+                <time datetime="2013-04-16T04:24:45+00:00">2013-04-16</time>
+                
+                  <div class="changeset">
+                  <a href="/galaxyp/galaxyp-toolshed-proteinpilot/commits/51a040d6310f38d2fb138acf6fb0a945a4532844" class="changeset-hash">51a040d</a>
+                  -
+                  
+                    
+                      Use config file to store input names and paths. This results in dramatically smaller command-lines (worry we are hitting the upperlimit of what Windows allows).
+                    
+                  
+                  </div>
+                
+                
+              </article>
+            
+
+              
+            
+          
+          
+        
+      
+    
+  
+    
+      
+        
+          
+            
+              </article>
+            
+            
+            
+              
+              <article class="news-item commit">
+                <span class="icon commit"></span>
+                
+
+
+  <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&amp;s=32" class="avatar avatar32" /></a>
+
+
+                <p>
+                  Commits by 
+
+  <a href="/jmchilton">John Chilton</a>
+
+                  were pushed to 
+
+
+<a href="/galaxyp/galaxyp-toolshed-proteinpilot" title="galaxyp/galaxyp-toolshed-proteinpilot">galaxyp/galaxyp-toolshed-proteinpilot</a>
+
+
+                </p>
+                <time datetime="2013-02-08T18:44:07+00:00">2013-02-08</time>
+                <div class="changeset">
+                  <a href="/galaxyp/galaxyp-toolshed-proteinpilot/commits/83f810baa907de50e87aa2efde99e088" class="changeset-hash">83f810b</a>
+                  -
+                  
+                    Add None as digestion option.
+                  
+                </div>
+            
+          
+          
+        
+      
+    
+  
+    
+      
+        
+          
+            
+              <div class="changeset">
+                <a href="/galaxyp/galaxyp-toolshed-proteinpilot/commits/d2a889605d117c8bca26124d372841c1" class="changeset-hash">d2a8896</a>
+                -
+                
+                  Initial commit.
+                
+              </div>
+            
+          
+          
+        
+      
+    
+  
+    
+      
+        
+          
+            
+              </article>
+            
+            
+            
+              
+                
+                  
+
+            <article class="news-item create">
+              <span class="icon create"></span>
+              
+
+
+  <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&amp;s=32" class="avatar avatar32" /></a>
+
+
+              
+              <p>
+                
+
+  <a href="/jmchilton">John Chilton</a>
+
+                created 
+
+
+<a href="/galaxyp/galaxyp-toolshed-proteinpilot" title="galaxyp/galaxyp-toolshed-proteinpilot">galaxyp/galaxyp-toolshed-proteinpilot</a>
+
+</p>
+    
+    
+              <time datetime="2012-08-13T18:27:01+00:00">2012-08-13</time>
+    
+
+                
+              
+            
+          
+          
+            </article>
+          
+        
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+            
+              data-command="https://bitbucket.org/galaxyp/galaxyp-toolshed-proteinpilot"
+            
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+            <dd><a href="/galaxyp">galaxyp</a></dd>
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+            <dd>Public</dd>
+
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+
+            
+
+            <dt>Last updated</dt>
+            <dd><time datetime="2013-06-20T16:34:36.195974">16 minutes ago</time></dd>
+
+            <dt>Created</dt>
+            <dd><time datetime="2012-08-13T20:27:01.972536">2012-08-13</time></dd>
+
+            <dt>Size</dt>
+            <dd>
+              19.2 KB
+              <a rel="nofollow"
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+                  href="/galaxyp/galaxyp-toolshed-proteinpilot/get/478c9dfebeb1.zip"
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