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comparison msnbase_readmsdata.xml @ 15:b25a582ab6c1 draft

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
author workflow4metabolomics
date Mon, 15 Jul 2024 15:56:53 +0000
parents cdebdb178031
children 733d32b30aff
comparison
equal deleted inserted replaced
14:cdebdb178031 15:b25a582ab6c1
1 <tool id="msnbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@+galaxy0"> 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>
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"): 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"):
16 #if $os.path.islink(str($input)) 16 #if $os.path.islink(str($input))
17 #set $source = $os.readlink(str($input)) 17 #set $source = $os.readlink(str($input))
18 singlefile_galaxyPath '$source' singlefile_sampleName '$os.path.basename($source)' 18 singlefile_galaxyPath '$source' singlefile_sampleName '$os.path.basename($source)'
19 #else 19 #else
20 singlefile_galaxyPath '$input' singlefile_sampleName '$input.name' 20 singlefile_galaxyPath '$input' singlefile_sampleName '$input.element_identifier'
21 #end if 21 #end if
22 #else 22 #else
23 zipfile '$input' 23 zipfile '$input'
24 #end if 24 #end if
25 25
26 @COMMAND_LOG_EXIT@ 26 @COMMAND_LOG_EXIT@
27 ]]></command> 27 ]]></command>
28 28
29 <inputs> 29 <inputs>
30 30
31 <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" label="File(s) from your history containing your chromatograms" help="Single file mode for the following formats: mzxml, mzml, mzdata and netcdf. Zip file mode for the following formats: no_unzip.zip, zip. See the help section below." /> 31 <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,zip" label="File(s) from your history containing your chromatograms" help="Single file mode for the following formats: mzxml, mzml, mzdata and netcdf. Zip file mode for the following formats: zip. See the help section below." />
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> 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" /> 53 </test>
57 </test> 54 <test expect_num_outputs="1">
58 <test>
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" />
62 <has_text text="ko15.CDF" /> 58 <has_text text="ko15.CDF" />
63 <has_text text="featureNames: F1.S0001 F1.S0002 ... F1.S1278 (1278 total)" /> 59 <has_text text="featureNames: F1.S0001 F1.S0002 ... F1.S1278 (1278 total)" />
121 **Upstream tools** 117 **Upstream tools**
122 118
123 ========================= ========================================== 119 ========================= ==========================================
124 Name Format 120 Name Format
125 ========================= ========================================== 121 ========================= ==========================================
126 Upload File mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip 122 Upload File mzxml,mzml,mzdata,netcdf,zip
127 ========================= ========================================== 123 ========================= ==========================================
128 124
129 The easier way to process is to create a Dataset Collection of the type List 125 The easier way to process is to create a Dataset Collection of the type List
130 126
131 **Downstream tools** 127 **Downstream tools**
183 179
184 Create your zip file (*e.g.* arabidopsis.zip). 180 Create your zip file (*e.g.* arabidopsis.zip).
185 181
186 **Step 3 : Uploading it to our Galaxy server** 182 **Step 3 : Uploading it to our Galaxy server**
187 183
188 If your zip file is less than 2Gb, you can use the Get Data tool to upload it.
189
190 Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO_ on workflow4metabolomics.org.
191
192 .. _HOWTO: http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf
193
194 For more information, do not hesitate to send us an email at supportATworkflow4metabolomics.org.
195
196 Advices for converting your files into mzXML format (XCMS input) 184 Advices for converting your files into mzXML format (XCMS input)
197 ---------------------------------------------------------------- 185 ----------------------------------------------------------------
198 186
199 We recommend you to convert your raw files into **mzXML** in centroid mode (smaller files); this way the files will be compatible with the xmcs centWave algorithm. 187 We recommend you to convert your raw files into **mzXML** in centroid mode (smaller files); this way the files will be compatible with the xmcs centWave algorithm.
200 188