diff mothur/tools/mothur/align.check.xml @ 2:e990ac8a0f58

Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository

--- a/mothur/tools/mothur/align.check.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/align.check.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="mothur_align_check" name="Align.check" version="1.16.0">
+<tool id="mothur_align_check" name="Align.check" version="1.19.0">
  <description>Calculate the number of potentially misaligned bases</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -6,16 +6,27 @@
    --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.align\.check$:'$out_file
    --outputdir='$logfile.extra_files_path'
    --fasta=$fasta
-   --map=$map
+   --map=$ss.map
  </command>
   <inputs>
-   <param name="fasta" type="data" format="align" label="fasta - Sequences"/>
-   <param name="map" type="select" label="map - Select a secondary structure map" help="Contact Galaxy team for additions">
-    <options from_file="mothur_map.loc">
-     <column name="name" index="0" />
-     <column name="value" index="1" />
-    </options>
-   </param>
+   <param name="fasta" type="data" format="align" label="fasta - Aligned Sequences"/>
+   <conditional name="ss">
+    <param name="source" label="Select Secondary Structure Map from" type="select">
+     <option value="cached">Cached Secondary Structure Maps</option>
+     <option value="history">Your History</option>
+    </param>
+    <when value="cached">
+     <param name="map" type="select" label="map - Select a secondary structure map" help="Contact Galaxy team for additions">
+      <options from_file="mothur_map.loc">
+       <column name="name" index="0" />
+       <column name="value" index="1" />
+      </options>
+     </param>
+    </when>
+    <when value="history">
+     <param name="map" format="map" type="data" label="Secondary Structure Map" />
+    </when>
+   </conditional>
   </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
@@ -37,8 +48,9 @@
 
 **Command Documenation**
 
-The align.check_ command allows you to calculate the number of potentially misaligned bases in a 16S rRNA gene sequence alignment.
+The align.check_ command allows you to calculate the number of potentially misaligned bases in a 16S rRNA gene sequence alignment using a secondary_structure_map_.  If you are familiar with the editor window in ARB, this is the same as counting the number of ~, #, -, and = signs.  
 
+.. _secondary_structure_map: http://www.mothur.org/wiki/Secondary_structure_map
 .. _align.check: http://www.mothur.org/wiki/Align.check
 
  </help>