Mercurial > repos > lecorguille > msnbase_readmsdata

annotate msnbase_readmsdata.xml @ 14:cdebdb178031 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dff3ac53c7c305ff263e6358308db48cf9ed4e27"
author workflow4metabolomics
date Mon, 12 Apr 2021 09:34:31 +0000
parents cda005bc221c
children b25a582ab6c1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
14
cdebdb178031 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dff3ac53c7c305ff263e6358308db48cf9ed4e27"
workflow4metabolomics
parents: 13
diff changeset
1 <tool id="msnbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@+galaxy0">
6
9bfe06bed015 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bd62e55afae8b1ea7dd39b5579dea6a0e7bc5d61
lecorguille
parents: 5
diff changeset
2 <description>Imports mass-spectrometry data files</description>
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
3
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
4 <macros>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
5 <import>macros.xml</import>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
6 <import>macros_msnbase.xml</import>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
7 </macros>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
8
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
9 <expand macro="requirements"/>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
10 <expand macro="stdio"/>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
11
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
12 <command><![CDATA[
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
13 @COMMAND_RSCRIPT@/msnbase_readmsdata.r
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
14
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
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"):
12
d1ec753f586f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3621a0c0a3a089fdb8973ae15a5614f32fa1d8df"
workflow4metabolomics
parents: 11
diff changeset
16 #if $os.path.islink(str($input))
d1ec753f586f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3621a0c0a3a089fdb8973ae15a5614f32fa1d8df"
workflow4metabolomics
parents: 11
diff changeset
17 #set $source = $os.readlink(str($input))
d1ec753f586f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3621a0c0a3a089fdb8973ae15a5614f32fa1d8df"
workflow4metabolomics
parents: 11
diff changeset
18 singlefile_galaxyPath '$source' singlefile_sampleName '$os.path.basename($source)'
d1ec753f586f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3621a0c0a3a089fdb8973ae15a5614f32fa1d8df"
workflow4metabolomics
parents: 11
diff changeset
19 #else
d1ec753f586f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3621a0c0a3a089fdb8973ae15a5614f32fa1d8df"
workflow4metabolomics
parents: 11
diff changeset
20 singlefile_galaxyPath '$input' singlefile_sampleName '$input.name'
d1ec753f586f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3621a0c0a3a089fdb8973ae15a5614f32fa1d8df"
workflow4metabolomics
parents: 11
diff changeset
21 #end if
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
22 #else
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
23 zipfile '$input'
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
24 #end if
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
25
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
26 @COMMAND_LOG_EXIT@
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
27 ]]></command>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
28
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
29 <inputs>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
30
5
8705b9de3e6c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 4
diff changeset
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." />
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
32
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
33 </inputs>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
34
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
35 <outputs>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
36 <data name="xsetRData" format="rdata.msnbase.raw" label="${input.name.rsplit('.',1)[0]}.raw.RData" from_work_dir="readmsdata.RData" />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
37 <data name="sampleMetadata" format="tabular" label="${input.name.rsplit('.',1)[0]}.sampleMetadata.tsv" from_work_dir="sampleMetadata.tsv" >
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
38 <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
39 </data>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
40 </outputs>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
41
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
42 <tests>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
43
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
44 <test>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
45 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
46 <assert_stdout>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
47 <has_text text="rowNames: faahKO_reduce/KO/ko15.CDF faahKO_reduce/KO/ko16.CDF" />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
48 <has_text text="faahKO_reduce/WT/wt15.CDF faahKO_reduce/WT/wt16.CDF" />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
49 <has_text text="featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)" />
14
cdebdb178031 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dff3ac53c7c305ff263e6358308db48cf9ed4e27"
workflow4metabolomics
parents: 13
diff changeset
50 <has_text text="fvarLabels: fileIdx spIdx ... spectrum (33 total)" />
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
51 <has_text text="faahKO_reduce/KO/ko15.CDF ko15 KO" />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
52 <has_text text="faahKO_reduce/KO/ko16.CDF ko16 KO" />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
53 <has_text text="faahKO_reduce/WT/wt15.CDF wt15 WT" />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
54 <has_text text="faahKO_reduce/WT/wt16.CDF wt16 WT" />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
55 </assert_stdout>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
56 <output name="sampleMetadata" value="sampleMetadata.tsv" />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
57 </test>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
58 <test>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
59 <param name="input" value="ko15.CDF" ftype="netcdf" />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
60 <assert_stdout>
13
cda005bc221c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 12
diff changeset
61 <has_text text="rowNames: ko15.CDF" />
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
62 <has_text text="ko15.CDF" />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
63 <has_text text="featureNames: F1.S0001 F1.S0002 ... F1.S1278 (1278 total)" />
14
cdebdb178031 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dff3ac53c7c305ff263e6358308db48cf9ed4e27"
workflow4metabolomics
parents: 13
diff changeset
64 <has_text text="fvarLabels: fileIdx spIdx ... spectrum (33 total)" />
13
cda005bc221c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 12
diff changeset
65 <has_text text="ko15.CDF ko15 ." />
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
66 </assert_stdout>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
67 </test>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
68 <!-- DISABLE FOR TRAVIS
10
84533814b1d5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
lecorguille
parents: 6
diff changeset
69 Useful to generate test-data for the further steps
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
70 <test>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
71 <param name="input" value="ko16.CDF" ftype="netcdf" />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
72 <assert_stdout>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
73 <has_text text="rowNames: ./ko16.CDF" />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
74 <has_text text="ko16.CDF" />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
75 <has_text text="./ko16.CDF ko16 ." />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
76 </assert_stdout>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
77 </test>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
78 <test>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
79 <param name="input" value="wt15.CDF" ftype="netcdf" />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
80 <assert_stdout>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
81 <has_text text="rowNames: ./wt15.CDF" />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
82 <has_text text="wt15.CDF" />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
83 <has_text text="./wt15.CDF wt15 ." />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
84 </assert_stdout>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
85 </test>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
86 <test>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
87 <param name="input" value="wt16.CDF" ftype="netcdf" />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
88 <assert_stdout>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
89 <has_text text="rowNames: ./wt16.CDF" />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
90 <has_text text="wt16.CDF" />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
91 <has_text text="./wt16.CDF wt16 ." />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
92 </assert_stdout>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
93 </test>
10
84533814b1d5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
lecorguille
parents: 6
diff changeset
94 -->
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
95 </tests>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
96
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
97 <help><![CDATA[
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
98
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
99 @HELP_AUTHORS@
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
100
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
101 ==================
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
102 MSnbase readMSData
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
103 ==================
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
104
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
105 -----------
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
106 Description
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
107 -----------
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
108
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
109 Reads as set of XML-based mass-spectrometry data files and
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
110 generates an MSnExp object. This function uses the functionality
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
111 provided by the ‘mzR’ package to access data and meta data in
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
112 ‘mzData’, ‘mzXML’ and ‘mzML’.
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
113
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
114 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
115
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
116
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
117 -----------------
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
118 Workflow position
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
119 -----------------
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
120
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
121 **Upstream tools**
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
122
4
df53d666da13 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 2
diff changeset
123 ========================= ==========================================
df53d666da13 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 2
diff changeset
124 Name Format
df53d666da13 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 2
diff changeset
125 ========================= ==========================================
df53d666da13 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 2
diff changeset
126 Upload File mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip
df53d666da13 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 2
diff changeset
127 ========================= ==========================================
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
128
4
df53d666da13 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 2
diff changeset
129 The easier way to process is to create a Dataset Collection of the type List
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
130
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
131 **Downstream tools**
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
132
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
133 =========================== ==================== ====================
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
134 Name Output file Format
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
135 =========================== ==================== ====================
4
df53d666da13 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 2
diff changeset
136 xcms.findChromPeaks ``*``.raw.RData rdata.msnbase.raw
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
137 =========================== ==================== ====================
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
138
10
84533814b1d5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
lecorguille
parents: 6
diff changeset
139
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
140
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
141 **Example of a metabolomic workflow**
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
142
4
df53d666da13 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 2
diff changeset
143 .. image:: msnbase_readmsdata_workflow.png
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
144
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
145 ---------------------------------------------------
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
146
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
147
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
148
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
149 -----------
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
150 Input files
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
151 -----------
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
152
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
153 =========================== ==================================
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
154 Parameter : num + label Format
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
155 =========================== ==================================
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
156 OR : Zip file zip
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
157 --------------------------- ----------------------------------
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
158 OR : Single file mzXML, mzML, mzData, netCDF
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
159 =========================== ==================================
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
160
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
161 **Choose your inputs**
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
162
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
163 You have two methods for your inputs:
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
164
10
84533814b1d5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
lecorguille
parents: 6
diff changeset
165 | Single file (recommended): You can put a single file as input. That way, you will be able to launch several readMSData and findChromPeaks in parallel and use "findChromPeaks Merger" before groupChromPeaks.
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
166 | Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
167
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
168 Zip file: Steps for creating the zip file
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
169 -----------------------------------------
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
170
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
171 **Step1: Creating your directory and hierarchize the subdirectories**
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
172
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
173
5
8705b9de3e6c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 4
diff changeset
174 VERY IMPORTANT: If you zip your files under Windows, you must use the 7Zip_ software, otherwise your zip will not be well unzipped on the W4M platform (corrupted zip bug).
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
175
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
176 .. _7Zip: http://www.7-zip.org/
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
177
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
178 Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild):
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
179 arabidopsis/wild/01.raw
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
180 arabidopsis/mutant/01.raw
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
181
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
182 **Step2: Creating a zip file**
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
183
5
8705b9de3e6c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 4
diff changeset
184 Create your zip file (*e.g.* arabidopsis.zip).
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
185
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
186 **Step 3 : Uploading it to our Galaxy server**
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
187
5
8705b9de3e6c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 4
diff changeset
188 If your zip file is less than 2Gb, you can use the Get Data tool to upload it.
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
189
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
190 Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO_ on workflow4metabolomics.org.
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
191
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
192 .. _HOWTO: http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
193
5
8705b9de3e6c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 4
diff changeset
194 For more information, do not hesitate to send us an email at supportATworkflow4metabolomics.org.
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
195
5
8705b9de3e6c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 4
diff changeset
196 Advices for converting your files into mzXML format (XCMS input)
8705b9de3e6c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 4
diff changeset
197 ----------------------------------------------------------------
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
198
5
8705b9de3e6c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 4
diff changeset
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.
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
200
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
201 **We recommend you the following parameters:**
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
202
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
203 Use Filtering: **True**
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
204
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
205 Use Peak Picking: **True**
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
206
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
207 Peak Peaking -Apply to MS Levels: **All Levels (1-)** : Centroid Mode
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
208
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
209 Use zlib: **64**
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
210
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
211 Binary Encoding: **64**
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
212
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
213 m/z Encoding: **64**
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
214
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
215 Intensity Encoding: **64**
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
216
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
217
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
218 ------------
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
219 Output files
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
220 ------------
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
221
4
df53d666da13 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 2
diff changeset
222 xset.RData: rdata.msnbase.raw format
df53d666da13 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 2
diff changeset
223
5
8705b9de3e6c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 4
diff changeset
224 | Rdata file that is necessary in the second step of the workflow "xcms.findChromPeaks".
4
df53d666da13 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 2
diff changeset
225
df53d666da13 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 2
diff changeset
226 sampleMetadata.tsv (only when a zip is used)
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
227
5
8705b9de3e6c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 4
diff changeset
228 | Tabular file that contains for each sample its associated class and polarity (positive,negative and mixed).
8705b9de3e6c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 4
diff changeset
229 | This file is necessary in further steps of the workflow, as the Anova and PCA steps for example.
10
84533814b1d5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
lecorguille
parents: 6
diff changeset
230 | You get a sampleMetadata.tsv only if you use a zip. Otherwise, you have to provide one for the findChromPeaks Merger step.
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
231
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
232 ---------------------------------------------------
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
233
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
234 Changelog/News
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
235 --------------
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
236
14
cdebdb178031 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dff3ac53c7c305ff263e6358308db48cf9ed4e27"
workflow4metabolomics
parents: 13
diff changeset
237 .. _News: https://lgatto.github.io/MSnbase/news/index.html
cdebdb178031 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dff3ac53c7c305ff263e6358308db48cf9ed4e27"
workflow4metabolomics
parents: 13
diff changeset
238
cdebdb178031 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dff3ac53c7c305ff263e6358308db48cf9ed4e27"
workflow4metabolomics
parents: 13
diff changeset
239 **Version 2.16.1+galaxy0 - 08/04/2019**
cdebdb178031 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dff3ac53c7c305ff263e6358308db48cf9ed4e27"
workflow4metabolomics
parents: 13
diff changeset
240
cdebdb178031 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dff3ac53c7c305ff263e6358308db48cf9ed4e27"
workflow4metabolomics
parents: 13
diff changeset
241 - UPGRADE: upgrade the MSnbase version from 2.8.2 to 2.16.1 (see MSnbase News_). Almost all the new features may not concern our usage of MSnbase.
10
84533814b1d5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
lecorguille
parents: 6
diff changeset
242
11
144392dd4a31 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
lecorguille
parents: 10
diff changeset
243 **Version 2.8.2.1 - 30/04/2019**
144392dd4a31 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
lecorguille
parents: 10
diff changeset
244
144392dd4a31 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
lecorguille
parents: 10
diff changeset
245 - BUGFIX: remove the pre-compute of the chromatograms which was memory consuming. Now, only xcms plot chromatogram will generate the Chromatograms.
144392dd4a31 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
lecorguille
parents: 10
diff changeset
246
10
84533814b1d5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
lecorguille
parents: 6
diff changeset
247 **Version 2.8.2.0 - 08/04/2019**
84533814b1d5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
lecorguille
parents: 6
diff changeset
248
84533814b1d5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
lecorguille
parents: 6
diff changeset
249 - UPGRADE: upgrade the MSnbase version from 2.4.0 to 2.8.2 (see MSnbase News_). Almost all the new features may not concern our usage of MSnbase.
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
250
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
251 **Version 2.4.0.0 - 29/03/2018**
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
252
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
253 - NEW: a new dedicated tool to read the raw data. This function was previously included in xcms.findChromPeaks. This way, you will now be able to display TICs and BPCs before xcms.findChromPeaks.
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
254
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
255 ]]></help>
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
256
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
257 <expand macro="citation" />
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
258 </tool>