diff kraken-report.xml @ 2:45ced9c12e18 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit cb6ebb843c71dcfc73aa05cc616f8e3229170108-dirty

--- a/kraken-report.xml	Tue May 19 16:42:26 2015 -0400
+++ b/kraken-report.xml	Wed Jul 15 15:22:27 2015 -0400
@@ -1,6 +1,6 @@
-<tool id="kraken-report" name="Kraken-report" version="1.0.0">
+<tool id="kraken-report" name="Kraken-report" version="1.1.0">
     <description>
-        View a sample report of your classification
+        view a sample report of your classification
     </description>
     <macros>
         <import>macros.xml</import>
@@ -12,7 +12,7 @@
         ]]>
     </command>
     <inputs>
-        <param format="tabular" label="Input the Sequenced Kraken Output from your Current History" name="kraken_output" type="data" />
+        <param format="tabular" label="Kraken output" name="kraken_output" type="data" help="Select taxonomy classification produced by kraken"/>
         <expand macro="input_database" />
     </inputs>
     <outputs>
@@ -21,24 +21,22 @@
     <help>
 <![CDATA[
 
-***Note that the database used must be the same as the one used to generate
-the output file, or the report script may encounter problems.***
+.. class:: warningmark
 
+**Note**: the database used must be the same as the one used in the original Kraken run
 
+-----
 
-**The output of kraken-report is tab-delimited, with one line per taxon. The fields of the output, from left-to-right, are as follows:**
-
-    1)Percentage of reads covered by the clade rooted at this taxon
+**Output**
 
-    2)Number of reads covered by the clade rooted at this taxon
-
-    3)Number of reads assigned directly to this taxon
+The output of kraken-report is tab-delimited, with one line per taxon. The fields of the output, from left-to-right, are as follows::
 
-    4)A rank code, indicating (U)nclassified, (D)omain, (K)ingdom, (P)hylum, (C)lass, (O)rder, (F)amily, (G)enus, or (S)pecies. All other ranks are simply -.
-
-    5)NCBI taxonomy ID
-
-    6)Indented scientific name
+ 1. Percentage of reads covered by the clade rooted at this taxon
+ 2. Number of reads covered by the clade rooted at this taxon
+ 3. Number of reads assigned directly to this taxon
+ 4. A rank code, indicating (U)nclassified, (D)omain, (K)ingdom, (P)hylum, (C)lass, (O)rder, (F)amily, (G)enus, or (S)pecies. All other ranks are simply filled with a dash.
+ 5. NCBI taxonomy ID
+ 6. Indented scientific name
 
 The scientific names are indented using spaces, according to the tree
 structure specified by the taxonomy.