Mercurial > repos > lecorguille > msnbase_readmsdata

comparison msnbase_readmsdata.xml @ 16:733d32b30aff draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
author workflow4metabolomics
date Mon, 03 Feb 2025 14:43:08 +0000
parents b25a582ab6c1
children
comparison
equal deleted inserted replaced
15:b25a582ab6c1 16:733d32b30aff
1 <tool id="msnbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@+galaxy2"> 1 <tool id="msnbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@+galaxy3">
2 <description>Imports mass-spectrometry data files</description> 2 <description>Imports mass-spectrometry data files</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 <import>macros_msnbase.xml</import> 6 <import>macros_msnbase.xml</import>
7 </macros> 7 </macros>
8 8
9 <expand macro="requirements"/> 9 <expand macro="requirements"/>
10 <required_files>
11 <include path="msnbase_readmsdata.r" />
12 <include path="lib.r" />
13 </required_files>
10 <expand macro="stdio"/> 14 <expand macro="stdio"/>
11 15
12 <command><![CDATA[ 16 <command><![CDATA[
13 @COMMAND_RSCRIPT@/msnbase_readmsdata.r 17 @COMMAND_RSCRIPT@msnbase_readmsdata.r
14 18
15 #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"): 19 #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"):
16 #if $os.path.islink(str($input)) 20 #if $os.path.islink(str($input))
17 #set $source = $os.readlink(str($input)) 21 #set $source = $os.readlink(str($input))
18 singlefile_galaxyPath '$source' singlefile_sampleName '$os.path.basename($source)' 22 singlefile_galaxyPath '$source' singlefile_sampleName '$os.path.basename($source)'