Mercurial > repos > lecorguille > msnbase_readmsdata

comparison msnbase_readmsdata.xml @ 16:12def6edac2f draft

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 03db090375a4ceb553dbf5ae77ef3866e98fbe9e
author workflow4metabolomics
date Tue, 21 Nov 2023 09:44:25 +0000
parents 7faf9b2d83f6
children 35b6fe4d481c
comparison
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15:7faf9b2d83f6 16:12def6edac2f
1 <tool id="msnbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@+galaxy1"> 1 <tool id="msnbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@+galaxy2">
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>
32 32
33 </inputs> 33 </inputs>
34 34
35 <outputs> 35 <outputs>
36 <data name="xsetRData" format="rdata.msnbase.raw" label="${input.name.rsplit('.',1)[0]}.raw.RData" from_work_dir="readmsdata.RData" /> 36 <data name="xsetRData" format="rdata.msnbase.raw" label="${input.name.rsplit('.',1)[0]}.raw.RData" from_work_dir="readmsdata.RData" />
37 <data name="sampleMetadata" format="tabular" label="${input.name.rsplit('.',1)[0]}.sampleMetadata.tsv" from_work_dir="sampleMetadata.tsv" >
38 <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
39 </data>
40 </outputs> 37 </outputs>
41 38
42 <tests> 39 <tests>
43 40
44 <test expect_num_outputs="2"> 41 <test expect_num_outputs="1">
45 <param name="input" value="faahKO_reduce.zip" ftype="zip" /> 42 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
46 <assert_stdout> 43 <assert_stdout>
47 <has_text text="rowNames: faahKO_reduce/KO/ko15.CDF faahKO_reduce/KO/ko16.CDF" /> 44 <has_text text="rowNames: faahKO_reduce/KO/ko15.CDF faahKO_reduce/KO/ko16.CDF" />
48 <has_text text="faahKO_reduce/WT/wt15.CDF faahKO_reduce/WT/wt16.CDF" /> 45 <has_text text="faahKO_reduce/WT/wt15.CDF faahKO_reduce/WT/wt16.CDF" />
49 <has_text text="featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)" /> 46 <has_text text="featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)" />
51 <has_text text="faahKO_reduce/KO/ko15.CDF ko15 KO" /> 48 <has_text text="faahKO_reduce/KO/ko15.CDF ko15 KO" />
52 <has_text text="faahKO_reduce/KO/ko16.CDF ko16 KO" /> 49 <has_text text="faahKO_reduce/KO/ko16.CDF ko16 KO" />
53 <has_text text="faahKO_reduce/WT/wt15.CDF wt15 WT" /> 50 <has_text text="faahKO_reduce/WT/wt15.CDF wt15 WT" />
54 <has_text text="faahKO_reduce/WT/wt16.CDF wt16 WT" /> 51 <has_text text="faahKO_reduce/WT/wt16.CDF wt16 WT" />
55 </assert_stdout> 52 </assert_stdout>
56 <output name="sampleMetadata" value="sampleMetadata.tsv" />
57 </test> 53 </test>
58 <test expect_num_outputs="1"> 54 <test expect_num_outputs="1">
59 <param name="input" value="ko15.CDF" ftype="netcdf" /> 55 <param name="input" value="ko15.CDF" ftype="netcdf" />
60 <assert_stdout> 56 <assert_stdout>
61 <has_text text="rowNames: ko15.CDF" /> 57 <has_text text="rowNames: ko15.CDF" />