Mercurial > repos > recetox > msp_split

diff splitMSP.xml @ 0:ae0263faa819 draft default tip

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
author recetox
date Fri, 25 Mar 2022 15:38:00 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/splitMSP.xml	Fri Mar 25 15:38:00 2022 +0000
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+<tool id="splitmsp" name="Split MSP Spectra" version="0.1.0" python_template_version="3.5">
+    <creator>
+        <person
+            givenName="Wudmir"
+            familyName="Rojas"
+            url="https://github.com/wverastegui"
+            identifier="0000-0001-7036-9987" />
+        <person
+            givenName="Helge"
+            familyName="Hecht"
+            url="https://github.com/hechth"
+            identifier="0000-0001-6744-996X" />
+        <organization
+            url="https://www.recetox.muni.cz/"
+            email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
+            name="RECETOX MUNI"/>
+    </creator>
+    <description>Split MSP spectra file</description>
+    <requirements>
+         <requirement type="package" version="0.14.0">matchms</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python3  '$__tool_directory__/splitMSP.py'
+        --filename '$msp_input'
+        --outdir   'output' 
+    ]]></command>
+    <inputs>
+        <param type="data" name="msp_input" format="msp" 
+               help="Use keyword 'compound_name', 'compoundname' or 'name' to identify individual spectra."/>
+    </inputs>
+    <outputs>
+        <collection  format="msp" name="sample" type="list">
+            <discover_datasets pattern="__designation_and_ext__" ext="msp" directory="output"/>
+        </collection >
+    </outputs>
+    <tests>
+        <test>
+            <param name="msp_input" value="sample_input.msp"  />
+            <output_collection name="sample" type="list">
+                <element name="1NITROPYRENE"         file="1NITROPYRENE.msp"         ftype="msp" compare="contains"/>
+                <element name="35DICHLOROPHENOL"     file="35DICHLOROPHENOL.msp"     ftype="msp" compare="contains"/>
+                <element name="34DICHLOROPHENOL"     file="34DICHLOROPHENOL.msp"     ftype="msp" compare="contains"/>
+                <element name="26DICHLOROPHENOL"     file="26DICHLOROPHENOL.msp"     ftype="msp" compare="contains"/>
+                <element name="25DICHLOROPHENOL"     file="25DICHLOROPHENOL.msp"     ftype="msp" compare="contains"/>
+                <element name="24DINITROPHENOL"      file="24DINITROPHENOL.msp"      ftype="msp" compare="contains"/>
+                <element name="24DICHLOROPHENOL"     file="24DICHLOROPHENOL.msp"     ftype="msp" compare="contains"/>
+                <element name="246TRICHLOROPHENOL"   file="246TRICHLOROPHENOL.msp"   ftype="msp" compare="contains"/>
+                <element name="245TRICHLOROPHENOL"   file="245TRICHLOROPHENOL.msp"   ftype="msp" compare="contains"/>
+                <element name="23DICHLOROPHENOL"     file="23DICHLOROPHENOL.msp"     ftype="msp" compare="contains"/>
+            </output_collection>
+        </test>
+    </tests> 
+    <help><![CDATA[
+        Splitmsp handles input/output files in MSP format using the matchms.importing and matchms.exporting modules (https://matchms.readthedocs.io/en/latest/index.html).
+    ]]></help>
+</tool>
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