diff metaphlan_to_phyloxml.xml @ 5:73f082e9fa2d

Set of improvements and fixes from Nicola Soranzo changeset: 9:c3dae016a3eb files: metaphlan.xml description: Update citation changeset: 8:f58b66b4e5fc files: metaphlan.xml description: Add select lists for -t and --tax_lev options Also some small fixes changeset: 7:94a2b29778b7 files: metaphlan_to_phyloxml.xml description: Clarify that only result of rel_ab analysis is accepted as input changeset: 6:b0eba028dee8 files: metaphlan.xml metaphlan_to_phyloxml.xml description: Fix whitespaces changeset: 5:4340075c8a93 files: tool_dependencies.xml description: Correct metaphlan clone URL to avoid a redirect changed metaphlan.xml changed metaphlan_to_phyloxml.xml changed tool_dependencies.xml

--- a/metaphlan_to_phyloxml.xml	Thu Oct 11 12:01:20 2012 -0500
+++ b/metaphlan_to_phyloxml.xml	Sun Dec 23 18:46:23 2012 +0100
@@ -1,17 +1,15 @@
 <tool id="meta_to_phylo" name="MetaPhlAn to PhyloXML" version="1.0.0">
- <description>Converter</description>
- <command interpreter="python">
-metaphlan_to_phyloxml.py $input $output
- </command>
- <inputs>
-  <param name="input" type="data" format="tabular" label="Input MetaPhlAn File"/>
- </inputs>
- <outputs>
+  <description>converter</description>
+  <command interpreter="python">metaphlan_to_phyloxml.py $input $output</command>
+  <inputs>
+    <param name="input" type="data" format="tabular" label="MetaPhlAn relative abundances"/>
+  </inputs>
+  <outputs>
     <data format="xml" name="output" label="${tool.name} on ${on_string}" /> 
- </outputs>
- <tests>
- </tests>
- <help>
-  MetaPhlAn to PhyloXML Converter
- </help>
+  </outputs>
+  <tests>
+  </tests>
+  <help>
+This tool converts the results of metagonome profiling performed with MetaPhlAn from tabular to PhyloXML format. The tool accepts as input only the result of rel_ab analysis (profiling in terms of relative abundaces), not reads_map or clade_profiles analysis.
+  </help>
 </tool>