changeset 0:e6fada5ebec4 draft

planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Mon May 18 00:33:22 2015 -0400
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+SpectraST
+=========
+
+Galaxy wrappers for SpectraST
+
+These wrappers are experimental.  The plan is to divide SpectraST into 3 tools, create, filter and search, each with its own wrapper
+
+Requirements
+------------
+
+This package uses protk_ and the trans_proteomic_pipeline_ which need to be present in order for the tool to work.
+
+.. _protk: https://github.com/iracooke/protk
+.. _trans_proteomic_pipeline: http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP
+
+There are two ways you can satify these dependencies (choose one):
+
+1. **Manual Install:** Details on how to install protk_ and the trans_proteomic_pipeline_ manually are available here_.
+
+2. **Use Docker:** These tools are designed to run inside a docker_ container. If your galaxy supports `running tools within a docker container`__ you don't need to worry about dependencies. Simply install and things should just work.  The docker container itself is versioned and new versions of this tool will automatically download an update to the container if needed.
+
+.. _docker: https://www.docker.com/
+.. _here: https://github.com/iracooke/protk/#galaxy-integration
+.. _container: https://wiki.galaxyproject.org/Admin/Tools/Docker
+__ container_
+
+
+Further Info
+------------
+
+The source code for this tool and other protk galaxy tools is on github_.  Please visit the github page to contribute to the project or to `report an issue`__ 
+
+.. _github: https://github.com/iracooke/protk-galaxytools
+.. _issue: https://github.com/iracooke/protk-galaxytools/issues
+__ issue_
+
+Please visit the SpectraST_ website for details of the SpectraST tool itself
+
+.. _SpectraST: http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Mon May 18 00:33:22 2015 -0400
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+<?xml version="1.0"?>
+<repositories description="Proteomics datatypes">
+    <repository changeset_revision="9cfabf0b942d" name="proteomics_datatypes" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+ </repositories>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spectrast_create.xml	Mon May 18 00:33:22 2015 -0400
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+<tool id="spectrast_create_1" name="SpectraST Create" version="1.0.0">
+    <requirements>
+        <container type="docker">iracooke/protk-1.4.2</container>
+        <requirement type="package" version="1.4">protk</requirement>
+        <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
+   </requirements>
+   
+	<description>Create Spectral Libraries</description>
+
+	<command>
+        spectrast_create.rb --galaxy 
+
+        #for $pepxml_file in $pepxml_files:
+        ${pepxml_file}
+        #end for
+
+        --spectrum-files='$spectrum_files'
+
+        --predicate 'Protein!~$decoy_prefix_string'
+
+        --p-thresh $p_thresh
+
+        --instrument-acquisition $instrument_acquisition
+
+        $input_file -o output
+
+	</command>
+
+	<inputs>
+
+        <param name="pepxml_files" multiple="true" type="data" format="pepxml" label="PepXML Files to use in library generation" help=""/>
+	
+        <param name="spectrum_files" multiple="true" type="data" format="mzml" label="Data files containing spectra referred to in pepxml files" help=""/>
+
+        <param name="decoy_prefix_string" help="String to identify decoys. All decoys wil be excluded" type="text" value="decoy" label="Decoy String" size="20"/> 
+
+        <param name="instrument_acquisition" help="Set the instrument and acquisition settings of the spectra (in case not specified in data files).
+                                 Examples: CID, ETD, CID-QTOF, HCD. The latter two are treated as high-mass accuracy spectra." type="text" value="CID-QTOF" label="Decoy String" size="20"/>
+
+        <param name="p_thresh" help="Matches scoring less than this value are discarded" type="float" value="0.95" min="0" max="1" label="Probability Threshold"/>
+
+	
+    </inputs>
+
+      <outputs>
+        <data format="splib" name="output" metadata_source="input_file" from_work_dir="output.splib"/>
+      </outputs>
+
+</tool>