annotate msconvert.xml @ 17:ab6c14374bc0 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit e3d24f3dc7a9812f8fa4447c9391e5bd3b5d4dc6
author galaxyp
date Thu, 15 Aug 2024 16:19:28 +0000
parents 545054b15d7c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
17
ab6c14374bc0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit e3d24f3dc7a9812f8fa4447c9391e5bd3b5d4dc6
galaxyp
parents: 16
diff changeset
1 <tool id="msconvert" name="msconvert" version="@VERSION@.4">
16
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
2 <description>Convert and/or filter mass spectrometry files</description>
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
3 <macros>
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
4 <import>msconvert_macros.xml</import>
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
5 </macros>
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
6 <xrefs>
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
7 <xref type="bio.tools">msconvert</xref>
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
8 </xrefs>
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
9 <requirements>
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
10 <container type="docker">chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:@FULL_VERSION@</container>
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
11 </requirements>
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
12 <stdio>
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
13 <regex match="Error writing run" source="stderr" level="fatal" description="Could not convert. Check stderr." />
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
14 </stdio>
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
15 <expand macro="msconvertCommand" />
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
16 <inputs>
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
17 <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" />
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
18 <expand macro="msconvertInputParameters" />
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
19 </inputs>
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
20 <expand macro="msconvertOutput" />
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
21 <tests>
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
22 <expand macro="msconvert_tests" />
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
23 </tests>
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
24 <help><![CDATA[
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
25 **What it does**
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
26
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
27 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.
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
28
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
29 You can view the original documentation here_.
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
30
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
31 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
32 ]]></help>
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
33 <expand macro="citations" />
8
d2c61663e33c Uploaded
galaxyp
parents:
diff changeset
34 </tool>