# HG changeset patch
# User drosofff
# Date 1434792861 14400
# Node ID 8fe1c798372d8e462fb64a418b4e6776bb83bf8d
# Parent  118834adb4ce0040aed57b7a5334d86bf820b96b
planemo upload for repository https://bitbucket.org/drosofff/gedtools/

diff -r 118834adb4ce -r 8fe1c798372d cap3.xml
--- a/cap3.xml	Mon Jun 08 07:55:57 2015 -0400
+++ b/cap3.xml	Sat Jun 20 05:34:21 2015 -0400
@@ -1,10 +1,11 @@
-<tool id="cap3" name="cap3" version="1.0.1">
+<tool id="cap3" name="cap3" version="1.1.0">
 <description>Sequence Assembly tool</description>
     <requirements>
     	<requirement type="package" version="3">cap3</requirement>
     </requirements>
 <command>
 cap3 "$inputSequences" > "$cap3stdout";
+                cat "$inputSequences".cap.contigs "$inputSequences".cap.singlets > $contigsandsinglets
                 mv "$inputSequences".cap.contigs $contigs;
                 mv "$inputSequences".cap.contigs.qual $contigsqual;
                 mv "$inputSequences".cap.contigs.links $contigslink;
@@ -19,16 +20,65 @@
         </inputs>
 
 <outputs>
-        	<data format="txt" name="cap3stdout" label="${tool.name} on ${on_string}: Standard Output"/>
+                <data format="fasta" name="contigsandsinglets" label="${tool.name} on ${on_string}: Contigs and singlets" from_work_dir="${inputSequences}.cap.contigs" />
+        	    <data format="txt" name="cap3stdout" label="${tool.name} on ${on_string}: Standard Output" hidden="true"/>
                 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="${inputSequences}.cap.contigs" />
-                <data format="txt" name="contigsqual" label="${tool.name} on ${on_string}: Contigs Qual" from_work_dir="${inputSequences}.cap.contigs.qual" hidden="True" />
-                <data format="txt" name="contigslink" label="${tool.name} on ${on_string}: Contigs Link" from_work_dir="${inputSequences}.cap.contigs.links" hidden="True" />
-                <data format="txt" name="ace" label="${tool.name} on ${on_string}: Ace" from_work_dir="${inputSequences}.cap.ace" hidden="True" />
-                <data format="txt" name="info" label="${tool.name} on ${on_string}: Info" from_work_dir="${inputSequences}.cap.info" hidden="True" />
-                <data format="txt" name="singlets" label="${tool.name} on ${on_string}: Singlets" from_work_dir="${inputSequences}.cap.singlets" hidden="True" />
+                <data format="txt" name="contigsqual" label="${tool.name} on ${on_string}: Contigs Qual" from_work_dir="${inputSequences}.cap.contigs.qual" hidden="true" />
+                <data format="txt" name="contigslink" label="${tool.name} on ${on_string}: Contigs Link" from_work_dir="${inputSequences}.cap.contigs.links" hidden="true" />
+                <data format="txt" name="ace" label="${tool.name} on ${on_string}: Ace" from_work_dir="${inputSequences}.cap.ace" hidden="true" />
+                <data format="txt" name="info" label="${tool.name} on ${on_string}: Info" from_work_dir="${inputSequences}.cap.info" hidden="true" />
+                <data format="txt" name="singlets" label="${tool.name} on ${on_string}: Singlets" from_work_dir="${inputSequences}.cap.singlets" />
 </outputs>
 
+  <tests>
+    <test>
+      <param name="inputSequences" value="input.fa" ftype="fasta"/>
+      <output name="contigsandsinglets" file="contigsandsinglets.fa"/>
+      <output name="cap3stdout" file="cap3stdout.txt"/>
+      <output name="contigs" file="contigs.fa"/>
+      <output name="contigsqual" file="contigsqual.txt"/>
+      <output name="contigslink" file="contigslink.txt"/>
+      <output name="ace" file="ace.txt"/>
+      <output name="singlets" file="singlets.fa"/>
+    </test>
+  </tests>
+
+
 <help>
+**What it does**
+
+This tool is a CAP3 wrapper developed for the visitor2 set of worflows
+
+Under this conditions, it takes as input a set of blast hits in fasta format and performs CAP3 assembly on these sequences
+
+Standard CAP3 outputs (Standard Output, Contigs Qual, Contigs Link, Ace and Info) are kept hidden in the Galaxy history (feel free to reveal these hidden datasets).
+
+Standard CAP3 outputs Contigs and Singlets are returned in the history, as well as a merge of these two datasets (Contigs and singlets)
+
+**Acknowledgments**
+
+This Galaxy tool makes use of the `package_cap3_3`_ Galaxy package developed by jjohnson the galaxy tool `get_fasta_from_taxon`_.
+
+It is Copyright © 2014-2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_.
+
+.. _package_cap3_3: https://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_cap3_3
+.. _CNRS and University Pierre et Marie Curie: http://www.ibps.upmc.fr/en
+.. _MIT license: http://opensource.org/licenses/MIT
+
 
 </help>
+  <citations>
+      <citation type="bibtex">@article{Huang:1999wb,
+       author = {Huang, X and Madan, A},
+       title = {{CAP3: A DNA sequence assembly program.}},
+       journal = {Genome research},
+       year = {1999},
+       volume = {9},
+       number = {9},
+      pages = {868--877},
+      month = sep
+      }
+      </citation>
+  </citations>
+  
 </tool>
diff -r 118834adb4ce -r 8fe1c798372d test-data/ace.txt
diff -r 118834adb4ce -r 8fe1c798372d test-data/cap3stdout.txt
diff -r 118834adb4ce -r 8fe1c798372d test-data/contigs.fa
diff -r 118834adb4ce -r 8fe1c798372d test-data/contigsandsinglets.fa
diff -r 118834adb4ce -r 8fe1c798372d test-data/contigslink.txt
diff -r 118834adb4ce -r 8fe1c798372d test-data/contigsqual.txt
diff -r 118834adb4ce -r 8fe1c798372d test-data/singlets.fa