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comparison msnbase_readmsdata.xml @ 15:7faf9b2d83f6 draft

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
author workflow4metabolomics
date Mon, 11 Sep 2023 09:24:51 +0000
parents 11ab2081bd4a
children 12def6edac2f
comparison
equal deleted inserted replaced
14:11ab2081bd4a 15:7faf9b2d83f6
1 <tool id="msnbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@+galaxy0"> 1 <tool id="msnbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@+galaxy1">
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" />
39 </data> 39 </data>
40 </outputs> 40 </outputs>
41 41
42 <tests> 42 <tests>
43 43
44 <test> 44 <test expect_num_outputs="2">
45 <param name="input" value="faahKO_reduce.zip" ftype="zip" /> 45 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
46 <assert_stdout> 46 <assert_stdout>
47 <has_text text="rowNames: faahKO_reduce/KO/ko15.CDF faahKO_reduce/KO/ko16.CDF" /> 47 <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" /> 48 <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)" /> 49 <has_text text="featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)" />
53 <has_text text="faahKO_reduce/WT/wt15.CDF wt15 WT" /> 53 <has_text text="faahKO_reduce/WT/wt15.CDF wt15 WT" />
54 <has_text text="faahKO_reduce/WT/wt16.CDF wt16 WT" /> 54 <has_text text="faahKO_reduce/WT/wt16.CDF wt16 WT" />
55 </assert_stdout> 55 </assert_stdout>
56 <output name="sampleMetadata" value="sampleMetadata.tsv" /> 56 <output name="sampleMetadata" value="sampleMetadata.tsv" />
57 </test> 57 </test>
58 <test> 58 <test expect_num_outputs="1">
59 <param name="input" value="ko15.CDF" ftype="netcdf" /> 59 <param name="input" value="ko15.CDF" ftype="netcdf" />
60 <assert_stdout> 60 <assert_stdout>
61 <has_text text="rowNames: ko15.CDF" /> 61 <has_text text="rowNames: ko15.CDF" />
62 <has_text text="ko15.CDF" /> 62 <has_text text="ko15.CDF" />
63 <has_text text="featureNames: F1.S0001 F1.S0002 ... F1.S1278 (1278 total)" /> 63 <has_text text="featureNames: F1.S0001 F1.S0002 ... F1.S1278 (1278 total)" />
121 **Upstream tools** 121 **Upstream tools**
122 122
123 ========================= ========================================== 123 ========================= ==========================================
124 Name Format 124 Name Format
125 ========================= ========================================== 125 ========================= ==========================================
126 Upload File mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip 126 Upload File mzxml,mzml,mzdata,netcdf,zip
127 ========================= ========================================== 127 ========================= ==========================================
128 128
129 The easier way to process is to create a Dataset Collection of the type List 129 The easier way to process is to create a Dataset Collection of the type List
130 130
131 **Downstream tools** 131 **Downstream tools**
183 183
184 Create your zip file (*e.g.* arabidopsis.zip). 184 Create your zip file (*e.g.* arabidopsis.zip).
185 185
186 **Step 3 : Uploading it to our Galaxy server** 186 **Step 3 : Uploading it to our Galaxy server**
187 187
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) 188 Advices for converting your files into mzXML format (XCMS input)
197 ---------------------------------------------------------------- 189 ----------------------------------------------------------------
198 190
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. 191 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.
200 192