Mercurial > repos > galaxyp > decoyfasta

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COPYING	Sun Feb 21 11:25:25 2016 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Sun Feb 21 11:25:25 2016 -0500
@@ -0,0 +1,55 @@
+GalaxyP - TPP decoyFASTA
+========================
+
+* Home: <https://github.com/galaxyproteomics/tools-galaxyp/>
+* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/decoyfasta>
+* Tool ID: `decoyfasta`
+
+
+Description
+-----------
+
+decoyFASTA from the Trans-Proteomic Pipeline.
+
+See:
+
+* <http://www.proteomecenter.org/software.php>
+* <http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP>
+* <https://en.wikipedia.org/wiki/Trans-Proteomic_Pipeline>
+
+
+GalaxyP Community
+-----------------
+
+Current governing community policies for [GalaxyP](https://github.com/galaxyproteomics/) and other information can be found at:
+
+<https://github.com/galaxyproteomics>
+
+
+License
+-------
+
+Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below.
+
+To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty.
+
+You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>.
+
+You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission.
+
+
+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://github.com/galaxyproteomics/tools-galaxyp/>
+
+
+Authors
+-------
+
+Authors and contributors:
+
+* Cody Wang
+* Fred Sadler
+* John Chilton <jmchilton@gmail.com>
+* Minnesota Supercomputing Institute, Univeristy of Minnesota
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/decoyfasta.xml	Sun Feb 21 11:25:25 2016 -0500
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+<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
+reversed sequences to use as decoys for False Discovery Rate (FDR) estimation in protein search identification. This tool employs the decoyFASTA program from
+the Transproteomic Pipeline.
+
+------
+
+**Citation**
+
+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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/repository_dependencies.xml	Sun Feb 21 11:25:25 2016 -0500
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories>
+  <repository changeset_revision="349af9298ff1" name="proteomics_datatypes" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+</repositories>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/tool_dependencies.xml	Sun Feb 21 11:25:25 2016 -0500
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="trans_proteomic_pipeline" version="4.8.0">
+    <repository changeset_revision="3d56da50b195" name="package_tpp_4_8_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+  </package>
+</tool_dependency>