Mercurial > repos > galaxyp > mz_to_sqlite

comparison mz_to_sqlite.xml @ 5:9a1ced29b130 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 75b9f57bf0b41b2a0b1e1c9f73447a1125fc245e"
author galaxyp
date Wed, 08 Jul 2020 14:03:33 +0000
parents 2a8a9f07782e
children f52c286f7e0b
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4:2a8a9f07782e 5:9a1ced29b130
1 <tool id="mz_to_sqlite" name="mz to sqlite" version="2.0.4"> 1 <tool id="mz_to_sqlite" name="mz to sqlite" version="2.0.4+galaxy1">
2 <description>Extract mzIdentML and associated proteomics datasets into a SQLite DB</description> 2 <description>Extract mzIdentML and associated proteomics datasets into a SQLite DB</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.0.4">mztosqlite</requirement> 4 <requirement type="package" version="2.0.4">mztosqlite</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" level="fatal" description="Error Running mz_to_sqlite" /> 7 <exit_code range="1:" level="fatal" description="Error Running mz_to_sqlite" />
8 </stdio> 8 </stdio>
9 <command> 9 <command>
10 <![CDATA[ 10 <![CDATA[
11 mz_to_sqlite -Xms1g -Xmx6g 11 mz_to_sqlite
12 -numthreads "\${GALAXY_SLOTS:-4}" 12 -numthreads "\${GALAXY_SLOTS:-4}"
13 -dbname 'sqlite.db' 13 -dbname 'sqlite.db'
14 -mzid '$mzinput' 14 -mzid '$mzinput'
15 #if len($scanfiles) > 0: 15 #if len($scanfiles) > 0:
16 #set $files = " ".join(["'"+ a.strip() + "'" for a in str($scanfiles).split(',')]) 16 #set $files = " ".join(["'"+ a.strip() + "'" for a in str($scanfiles).split(',')])