diff msconvert.xml @ 16:545054b15d7c draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd

--- a/msconvert.xml	Mon Nov 30 16:01:10 2020 +0000
+++ b/msconvert.xml	Sun Mar 24 11:13:43 2024 +0000
@@ -1,25 +1,34 @@
-<tool id="msconvert" name="msconvert" version="@VERSION@.2">
-  <description>Convert and/or filter mass spectrometry files</description>
-  <macros>
-      <import>msconvert_macros.xml</import>
-  </macros>
-  <requirements>
-      <container type="docker">chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:@FULL_VERSION@</container>
-  </requirements>
-  <stdio>
-    <regex match="Error writing run" source="stderr" level="fatal" description="Could not convert. Check stderr." />
-  </stdio>
-  <expand macro="msconvertCommand" />
-  <inputs>
-      <param format="mzml,mzxml,mz5,mgf,ms2,thermo.raw,raw,wiff,wiff.tar,agilentbrukeryep.d.tar,agilentmasshunter.d.tar,brukerbaf.d.tar,brukertdf.d.tar,watersmasslynx.raw.tar" name="input" type="data" label="Input unrefined MS data" />
-      <expand macro="msconvertInputParameters" />
-  </inputs>
-  <expand macro="msconvertOutput" />
-  <tests>
-      <expand macro="msconvert_tests" />
-  </tests>
-  <help>
-      <expand macro="msconvert_help" />
-  </help>
-  <expand macro="citations" />
+<tool id="msconvert" name="msconvert" version="@VERSION@.3">
+    <description>Convert and/or filter mass spectrometry files</description>
+    <macros>
+        <import>msconvert_macros.xml</import>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">msconvert</xref>
+    </xrefs>
+    <requirements>
+        <container type="docker">chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:@FULL_VERSION@</container>
+    </requirements>
+    <stdio>
+        <regex match="Error writing run" source="stderr" level="fatal" description="Could not convert. Check stderr." />
+    </stdio>
+    <expand macro="msconvertCommand" />
+    <inputs>
+        <param format="mzml,mzxml,mz5,mgf,ms2,thermo.raw,raw,wiff,wiff.tar,agilentbrukeryep.d.tar,agilentmasshunter.d.tar,brukerbaf.d.tar,brukertdf.d.tar,watersmasslynx.raw.tar" name="input" type="data" label="Input unrefined MS data" />
+        <expand macro="msconvertInputParameters" />
+    </inputs>
+    <expand macro="msconvertOutput" />
+    <tests>
+        <expand macro="msconvert_tests" />
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+Converts mass spectrometry (MS) files: proprietary MS vendor formats can be converted to open MS formats (mzML, mzXML, MGF, MS1/MS2) and open formats can be converted to other open formats. Additional options such as filtering and/or precursor recalculation are available.
+
+You can view the original documentation here_.
+
+.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
+]]></help>
+    <expand macro="citations" />
 </tool>