# HG changeset patch
# User galaxyp
# Date 1522331510 14400
# Node ID c8895a92b74dedf8041115304439b9558e26032b

planemo upload for repository https://github.com/galaxyproteomics/protk-galaxytools/tree/master/spectrast commit 34735d62618a252173e3c90436f240659484727a

diff -r 000000000000 -r c8895a92b74d README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Thu Mar 29 09:51:50 2018 -0400
@@ -0,0 +1,39 @@
+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
diff -r 000000000000 -r c8895a92b74d spectrast_create.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spectrast_create.xml	Thu Mar 29 09:51:50 2018 -0400
@@ -0,0 +1,62 @@
+<tool id="spectrast_create_1" name="SpectraST Create" version="5.0.0">
+    <description>Create Spectral Libraries</description>
+    <requirements>
+        <!--
+        <container type="docker">iracooke/protk-1.4.3</container>
+        -->
+        <requirement type="package" version="1.4.4a">protk</requirement>
+        <requirement type="package" version="5.0.0">tpp</requirement>
+   </requirements>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Job Failed" />
+    </stdio>
+    <command>
+<![CDATA[
+        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
+        -o library
+
+        &&
+
+        mkdir -p $output.files_path
+
+        &&
+
+        cp library.splib library.spidx library.pepidx  $output.files_path/
+
+        &&
+
+        echo "Spectral Library Primary File" > $output
+]]>
+    </command>
+    <inputs>
+
+        <param name="pepxml_files" multiple="true" type="data" format="pepxml,peptideprophet_pepxml,interprophet_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" type="text" value="CID-QTOF" label="Decoy String" size="20" 
+            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."/>
+        <param name="p_thresh" type="float" value="0.99" min="0" max="1" label="Probability Threshold"
+            help="Matches scoring less than this value are discarded" />
+    </inputs>
+    <outputs>
+        <data format="splib" name="output"/>
+    </outputs>
+    <help>
+<![CDATA[
+**What it does**
+
+Create Spectral Libraries.
+
+]]>
+    </help>
+</tool>
diff -r 000000000000 -r c8895a92b74d spectrast_filter.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spectrast_filter.xml	Thu Mar 29 09:51:50 2018 -0400
@@ -0,0 +1,65 @@
+<tool id="spectrast_filter_1" name="SpectraST Filter" version="5.0.0">
+    <description>Filter and Manipulate Spectral Libraries</description>
+    <requirements>
+        <!--
+        <container type="docker">iracooke/protk-1.4.3</container>
+        -->
+        <requirement type="package" version="1.4.4a">protk</requirement>
+        <requirement type="package" version="5.0.0">tpp</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Job Failed" />
+    </stdio>
+    <command>
+<![CDATA[
+        spectrast_filter.rb  --merge $merge
+
+        #for $splib_file in $splib_files:
+            ${splib_file.extra_files_path}/library.splib
+        #end for
+
+        --replicates $replicates
+        -o library
+
+        &&
+
+        mkdir -p ${output.files_path}
+
+        &&
+
+        cp library.splib library.spidx library.pepidx  ${output.files_path}/
+
+        &&
+
+        echo "Spectral Library Primary File" > $output
+]]>
+    </command>
+    <inputs>
+        <param name="splib_files" multiple="true" type="data" format="splib" label="Spectral Libraries to operate on" help=""/>
+        <param name="merge" type="select" format="text">
+            <label>Merge Method</label>
+            <option value="U">Union</option>
+            <option value="S">Subtraction</option>
+            <option value="H">Subtraction of homologs</option>
+            <option value="A">Appending</option>
+        </param>
+
+        <param name="replicates" type="select" format="text">
+            <label>How to deal with replicate spectra</label>
+            <option value="None">Keep All</option>
+            <option value="C">Consensus</option>
+            <option value="B">Best replicate</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="splib" name="output"/>
+    </outputs>
+    <help>
+<![CDATA[
+**What it does**
+
+Filter and Manipulate Spectral Libraries
+
+]]>
+    </help>
+</tool>