diff emboss_showfeat.xml @ 10:d49956b87f7e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/emboss_showfeat.xml	Wed Feb 08 12:42:22 2017 -0500
@@ -0,0 +1,97 @@
+<tool id="EMBOSS: showfeat85" name="showfeat" version="5.0.0.1">
+  <!-- tool gives memory errors -->
+  <description>Show features of a sequence</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <code file="emboss_format_corrector.py" />
+  <command>showfeat -sequence '$input1' -outfile '$out_file1' -matchsource '$matchsource' -matchtype '$matchtype' -matchtag '$matchtag' -matchvalue '$matchvalue' -sort $sort -annotation '$annotation' -id
+  $id -description $description -scale $scale -width $width -collapse $collapse -forward $forward -reverse $reverse -unknown $unknown -strand $strand -source $source -position $position -type
+  $type -tags $tags -values $values -stricttags $stricttags -html $html_out1 -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="data" label="Sequences" />
+    <param name="html_out1" type="select" label="Format output as an HTML table">
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="matchsource" type="text" value="*" label="Feature source to match" />
+    <param name="matchtype" type="text" value="*" label="Feature type to match" />
+    <param name="matchtag" type="text" value="*" label="Feature tags to match" />
+    <param name="matchvalue" type="text" value="*" label="Tag values to match" />
+    <param name="sort" type="select" label="Sort by">
+      <option value="start">Start position</option>
+      <option value="source">Source</option>
+      <option value="type">Type</option>
+      <option value="nosort">No sorting done</option>
+      <option value="join">Join coding regions together</option>
+    </param>
+    <param name="annotation" type="text" value="" label="Regions to annotate by marking" />
+    <param name="id" type="select" label="Display the ID name of the sequence">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="description" type="select" label="Display the description of the sequence">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="scale" type="select" label="Display the scale line">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="width" type="integer" value="60" label="Screen width" />
+    <param name="collapse" type="select" label="Collapse features">
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="forward" type="select" label="Display forward sense features">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="reverse" type="select" label="Display reverse sense features">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="unknown" type="select" label="Display unknown sense features">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="strand" type="select" label="Display the strand of the features">
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="source" type="select" label="Display the source of the features">
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="position" type="select" label="Display the start and end position of the features">
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="type" type="select" label="Display the type of the features">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="tags" type="select" label="Display the tags and values of the features">
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="values" type="select" label="Display the tag values of the features">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="stricttags" type="select" label="Display only those tag/value pairs in a feature that match the specified tag and value">
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out_file1" format="showfeat" />
+  </outputs>
+  <help>
+    You can view the original documentation here_.
+
+    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/showfeat.html
+  </help>
+  <expand macro="citations" />
+</tool>