# HG changeset patch
# User galaxyp
# Date 1456071631 18000
# Node ID c15d72720643b6623fd5419dd42f544d2632f130
# Parent  b6b2ac0716ebc5d8b138a82d09c76205ac9f630a
planemo upload commit bdb474693831a3375db79755e88641ad32b3b4e6-dirty

diff -r b6b2ac0716eb -r c15d72720643 README.md
--- a/README.md	Wed Oct 08 13:35:25 2014 -0400
+++ b/README.md	Sun Feb 21 11:20:31 2016 -0500
@@ -1,7 +1,7 @@
 GalaxyP - TPP decoyFASTA
 ========================
 
-* Home: <https://bitbucket.org/galaxyp/decoyfasta>
+* Home: <https://github.com/galaxyproteomics/tools-galaxyp/>
 * Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/decoyfasta>
 * Tool ID: `decoyfasta`
 
@@ -21,9 +21,9 @@
 GalaxyP Community
 -----------------
 
-Current governing community policies for [GalaxyP](https://bitbucket.org/galaxyp/) and other information can be found at:
+Current governing community policies for [GalaxyP](https://github.com/galaxyproteomics/) and other information can be found at:
 
-<https://bitbucket.org/galaxyp/galaxyp>
+<https://github.com/galaxyproteomics>
 
 
 License
@@ -41,7 +41,7 @@
 Contributing
 ------------
 
-Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://bitbucket.org/galaxyp/galaxyp/CONTRIBUTORS.md> unless you opt-out.
+Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://github.com/galaxyproteomics/tools-galaxyp/>
 
 
 Authors
diff -r b6b2ac0716eb -r c15d72720643 tools/decoyfasta.xml
--- a/tools/decoyfasta.xml	Wed Oct 08 13:35:25 2014 -0400
+++ b/tools/decoyfasta.xml	Sun Feb 21 11:20:31 2016 -0500
@@ -1,50 +1,51 @@
-<tool id="decoyfasta" name="Create Decoy Database (reverse)" version="0.1.0">
-  <description>Creates a decoy search database by adding reverse
-  sequences to an existing database.</description>
-
-  <requirements>
-    <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement>
-  </requirements>
-
-  <command>
-    decoyFASTA ${input} ${output} ${include_original}
-    #if $freq_type.advanced == "yes"
-    -t${frequency} ${tag}
-    #for $extra_tag in $extra_tags
-    -t${extra_tag.frequency} ${extra_tag.tag}
-    #end for
-    #else
-    -t1 ${freq_type.tag}
-    #end if
-  </command>
-
-  <inputs>
-    <param format="fasta" name="input" type="data" label="FASTA Input" help="select input database from history in FASTA format" />
-    <param name="include_original" type="boolean" truevalue="" falsevalue="-no_orig" label="Include original entries in output database" checked="True" help="(default) keep checked in all standard searches" />
-    <conditional name="freq_type">
-      <param name="advanced" type="select" label="Specify advanced decoy frequency options?" help="&quot;Decoy Prefix&quot; will name the prefix of each decoy sequence, &quot;Frequency&quot; will specify how many decoy sequences are created">
-        <option value="no">No, just create database with one reversed sequence for every input sequence</option>
-        <option value="yes">Yes, I want to specify multiple prefixes and specific frequencies</option>
-      </param>
-      <when value="no">
-        <param name="tag" type="text" value="decoy_" label="Decoy Prefix"/>
-      </when>
-      <when value="yes">
-        <param name="tag" type="text" value="decoy_" label="Decoy Prefix"/>
-        <param name="frequency" type="integer" value="1" label="Decoy Frequency" />
-        <repeat name="extra_tags" title="Additional Decoy Tags">
-          <param name="tag" type="text" value="decoy_" label="Decoy Prefix"/>
-          <param name="frequency" type="integer" value="1" label="Decoy Frequency" />
-        </repeat>
-      </when>
-    </conditional>
-  </inputs>
-
-  <outputs>
-    <data format="fasta" name="output" />
-  </outputs>
-
+<tool id="decoyfasta" name="Create Decoy Database (reverse)" version="0.2.0">
+    <description>Creates a decoy search database by adding reverse
+    sequences to an existing database</description>
+    <requirements>
+        <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        decoyFASTA
+            ${input}
+            ${output}
+            ${include_original}
+            #if $freq_type.advanced == "yes"
+                -t${frequency} ${tag}
+                #for $extra_tag in $extra_tags
+                    -t${extra_tag.frequency} ${extra_tag.tag}
+                #end for
+            #else
+                -t1 ${freq_type.tag}
+            #end if
+]]>
+    </command>
+    <inputs>
+        <param format="fasta" name="input" type="data" label="FASTA Input" help="select input database from history in FASTA format" />
+        <param name="include_original" type="boolean" truevalue="" falsevalue="-no_orig" label="Include original entries in output database" checked="True" help="(default) keep checked in all standard searches" />
+        <conditional name="freq_type">
+            <param name="advanced" type="select" label="Specify advanced decoy frequency options?" help="&quot;Decoy Prefix&quot; will name the prefix of each decoy sequence, &quot;Frequency&quot; will specify how many decoy sequences are created">
+                <option value="no">No, just create database with one reversed sequence for every input sequence</option>
+                <option value="yes">Yes, I want to specify multiple prefixes and specific frequencies</option>
+            </param>
+            <when value="no">
+                <param name="tag" type="text" value="decoy_" label="Decoy Prefix"/>
+            </when>
+            <when value="yes">
+                <param name="tag" type="text" value="decoy_" label="Decoy Prefix"/>
+                <param name="frequency" type="integer" value="1" label="Decoy Frequency" />
+                <repeat name="extra_tags" title="Additional Decoy Tags">
+                    <param name="tag" type="text" value="decoy_" label="Decoy Prefix"/>
+                    <param name="frequency" type="integer" value="1" label="Decoy Frequency" />
+                </repeat>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="fasta" name="output" />
+    </outputs>
   <help>
+<![CDATA[
 **What it does**
 
 Given an input database, this tool will produce another database with
@@ -55,8 +56,10 @@
 
 **Citation**
 
-For the underlying tool, please cite `Proteomics. 2010 Mar;10(6):1150-9. A guided tour of the Trans-Proteomic Pipeline. Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, Sun Z, Nilsson E, Pratt B, Prazen B, Eng JK, Martin DB, Nesvizhskii AI, Aebersold R. PMID 20101611`
-
-If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/decoyfasta
-  </help>
+If you use this tool in Galaxy, please cite Chilton J, et al. https://github.com/galaxyproteomics/
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1002/pmic.200900375</citation>
+    </citations>
 </tool>
diff -r b6b2ac0716eb -r c15d72720643 tools/repository_dependencies.xml
--- a/tools/repository_dependencies.xml	Wed Oct 08 13:35:25 2014 -0400
+++ b/tools/repository_dependencies.xml	Sun Feb 21 11:20:31 2016 -0500
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories>
-  <repository changeset_revision="f66f8ca7b7b9" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
+  <repository changeset_revision="300fc3aa6954" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
 </repositories>
diff -r b6b2ac0716eb -r c15d72720643 tools/tool_dependencies.xml
--- a/tools/tool_dependencies.xml	Wed Oct 08 13:35:25 2014 -0400
+++ b/tools/tool_dependencies.xml	Sun Feb 21 11:20:31 2016 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="trans_proteomic_pipeline" version="4.6.3">
-    <repository changeset_revision="0bce36ee6bf2" name="package_tpp_4_6_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+  <package name="trans_proteomic_pipeline" version="4.8.0">
+    <repository changeset_revision="a7273394d858" name="package_tpp_4_8_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
 </tool_dependency>