diff Rooting/rooting.xml @ 10:c6640c49fd01 draft

planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac

--- a/Rooting/rooting.xml	Wed Feb 07 22:08:47 2018 -0500
+++ b/Rooting/rooting.xml	Mon Apr 16 09:00:24 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="sniplay_rooting" name="Rooting" version="1.0.3">
+<tool id="sniplay_rooting" name="Rooting" version="2.0.0">
     
     <!-- [REQUIRED] Tool description displayed after the tool name -->
     <description> Midpoint rooting of newick tree </description>
@@ -6,7 +6,7 @@
     <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
     <requirements>
         <requirement type="binary">perl</requirement>
-	<requirement type="package">Rootings_54.jar</requirement>
+        <requirement type="package" version="1.6.924">perl-bioperl</requirement>
     </requirements>
 
     <!-- [STRONGLY RECOMMANDED] Exit code rules -->
@@ -30,58 +30,44 @@
    
     <!-- [REQUIRED] Input files and tool parameters -->
     <inputs>
-	<param name="filein" type="data" format="nwk" optional="false" label="Fasta alignment input" />
+	<param name="filein" type="data" format="nwk,nhx" optional="false" label="Newick tree input" />
 	<param name="fileout_label" type="text" value="out tree" label="Output name" help="Output name for files" />
     </inputs> 
     
     <!-- [REQUIRED] Output files -->
     <outputs>
-	<data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
-	<data name="fileout" type="data" format="nwk" label="${fileout_label}" />
+	<data name="fileout_log" format="txt" label="${fileout_label}.log" />
+	<data name="fileout" format="nwk,nhx" label="${fileout_label}" />
     </outputs>
     
     <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
     <tests>
         <!-- [HELP] Test files have to be in the ~/test-data directory -->
-
         <test>
          <param name="filein" value="rooting-newick" />
          <output name="fileout" file="rooting-out_tree" />
         </test>
-
-        <!-- [HELP] Multiple tests can be defined with different parameters -->
-<!--
-        <test>
-        </test>
--->
     </tests>
     
     <!-- [OPTIONAL] Help displayed in Galaxy -->
-    <help>
-
+    <help><![CDATA[
 
 .. class:: infomark
 
 **Authors** Jean-François Dufayard, CIRAD, South Green platform
 
-
-.. class:: infomark
-
-**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
+ | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
 
 .. class:: infomark
 
-**Support** For any questions about Galaxy integration, please send an e-mail to [e-mail]
+**Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA)
 
 .. class:: infomark
 
-**Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
+**Support** For any questions about Galaxy integration, please send an e-mail to [e-mail]
 
 ---------------------------------------------------
 
-
-
-
 =======
 Rooting
 =======
@@ -92,27 +78,20 @@
 
   Compute a midpoint newick rooted tree.
 
-
------------------
-Workflow position
------------------
-
-**Upstream tool**
+------------
+Dependencies
+------------
+Bioperl
+        perl-bioperl_ 1.6.924, Conda version
 
-=========== ========================== =======
-Name            output file(s)         format 
-=========== ========================== =======
-fastme      Newick tree                Newick 
-=========== ========================== =======
-
-
+.. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl
 
 ----------
 Input file
 ----------
 
 Newick file
-	
+        Input tree file
 
 ----------
 Parameters
@@ -144,8 +123,8 @@
 Working example
 ---------------
 
-Input files
-===========
+Input file
+==========
 
 Newick file
 -----------
@@ -155,14 +134,14 @@
 	(((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ...
 
 
-Parameters
-==========
+Parameter
+=========
 
 Output name -> out tree
 
 
-Output files
-============
+Output file
+===========
 
 out tree
 --------
@@ -172,7 +151,7 @@
 	(ref:0.9384270000000001,(((((((((((((((((((((((((((((((((((IRAT257:0.044246,IRAT112:0.023421):0.009006,ARAGUAIA:0.093061):0.004662...
 	
 
-    </help>
+    ]]></help>
     <citations>
         <!-- [HELP] As DOI or BibTex entry -->
     	<citation type="bibtex">@article{Dereeper03062015,