Mercurial > repos > lecorguille > xcms_export_samplemetadata
annotate macros_xcms.xml @ 4:8c62030a1136 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
| author | lecorguille |
|---|---|
| date | Mon, 11 Feb 2019 06:16:45 -0500 |
| parents | e3c06320f884 |
| children | 45a1db23a4a5 |
| rev | line source |
|---|---|
|
0
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
1 <?xml version="1.0"?> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
2 <macros> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
3 |
|
4
8c62030a1136
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
lecorguille
parents:
0
diff
changeset
|
4 <token name="@WRAPPER_VERSION@">3.4.3</token> |
|
0
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
5 <xml name="requirements"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
6 <requirements> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
7 <requirement type="package" version="@WRAPPER_VERSION@">bioconductor-xcms</requirement> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
8 <requirement type="package" version="1.1_4">r-batch</requirement> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
9 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
10 <requirement type="package" version="6.0">unzip</requirement> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
11 <yield /> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
12 </requirements> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
13 </xml> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
14 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
15 <!-- FILE_LOAD for planemo test --> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
16 <token name="@COMMAND_FILE_LOAD@"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
17 #if $file_load_section.file_load_conditional.file_load_select == "yes": |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
18 #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"): |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
19 #set singlefile_galaxyPath = '|'.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] ) |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
20 #set singlefile_sampleName = '|'.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] ) |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
21 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
22 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName' |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
23 #else |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
24 zipfile '$file_load_section.file_load_conditional.input' |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
25 #end if |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
26 #end if |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
27 </token> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
28 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
29 <xml name="input_file_load"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
30 <section name="file_load_section" title="Resubmit your raw dataset or your zip file"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
31 <conditional name="file_load_conditional"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
32 <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message saying that your original dataset or zip file have been deleted on the server." > |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
33 <option value="no" >no need</option> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
34 <option value="yes" >yes</option> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
35 </param> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
36 <when value="no"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
37 </when> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
38 <when value="yes"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
39 <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." /> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
40 </when> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
41 </conditional> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
42 </section> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
43 </xml> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
44 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
45 <xml name="test_file_load_zip"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
46 <section name="file_load_section"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
47 <conditional name="file_load_conditional"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
48 <param name="file_load_select" value="yes" /> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
49 <param name="input" value="faahKO_reduce.zip" ftype="zip" /> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
50 </conditional> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
51 </section> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
52 </xml> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
53 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
54 <xml name="test_file_load_zip_sacuri"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
55 <section name="file_load_section"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
56 <conditional name="file_load_conditional"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
57 <param name="file_load_select" value="yes" /> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
58 <param name="input" value="sacuri_dir_root.zip" ftype="zip" /> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
59 </conditional> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
60 </section> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
61 </xml> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
62 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
63 <xml name="test_file_load_single"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
64 <section name="file_load_section"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
65 <conditional name="file_load_conditional"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
66 <param name="file_load_select" value="yes" /> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
67 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" /> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
68 </conditional> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
69 </section> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
70 </xml> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
71 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
72 <xml name="test_file_load_single_ko15"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
73 <section name="file_load_section"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
74 <conditional name="file_load_conditional"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
75 <param name="file_load_select" value="yes" /> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
76 <param name="input" value="ko15.CDF" ftype="netcdf" /> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
77 </conditional> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
78 </section> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
79 </xml> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
80 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
81 <!-- PEAKLIST --> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
82 <token name="@COMMAND_PEAKLIST@"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
83 #if $peaklist.peaklistBool |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
84 convertRTMinute $peaklist.convertRTMinute |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
85 numDigitsMZ $peaklist.numDigitsMZ |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
86 numDigitsRT $peaklist.numDigitsRT |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
87 intval $peaklist.intval |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
88 naTOzero $peaklist.naTOzero |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
89 #end if |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
90 </token> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
91 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
92 <xml name="input_peaklist"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
93 <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
94 <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" /> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
95 <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" /> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
96 <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
97 <option value="into" selected="true">into</option> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
98 <option value="maxo">maxo</option> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
99 <option value="intb">intb</option> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
100 </param> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
101 <param name="naTOzero" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Replace the remain NA by 0 in the dataMatrix" help="Rather mandatory for some downstream statistical steps"/> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
102 </xml> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
103 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
104 <xml name="input_peaklist_section"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
105 <section name="peaklist" title="Peak List" expanded="True"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
106 <param name="peaklistBool" type="hidden" label="Get the Peak List" value="True" /> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
107 <expand macro="input_peaklist"/> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
108 </section> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
109 </xml> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
110 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
111 <xml name="input_peaklist_conditional"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
112 <conditional name="peaklist"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
113 <param name="peaklistBool" type="boolean" label="Get the Peak List" /> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
114 <when value="true"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
115 <expand macro="input_peaklist"/> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
116 </when> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
117 <when value="false" /> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
118 </conditional> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
119 </xml> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
120 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
121 <xml name="output_peaklist" token_function=""> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
122 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" > |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
123 <filter>(peaklist['peaklistBool'])</filter> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
124 </data> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
125 <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" from_work_dir="dataMatrix.tsv" > |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
126 <filter>(peaklist['peaklistBool'])</filter> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
127 </data> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
128 </xml> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
129 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
130 <token name="@HELP_PEAKLIST@"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
131 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
132 Get a Peak List |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
133 --------------- |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
134 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
135 If 'true', the module generates two additional files corresponding to the peak list: |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
136 - the variable metadata file (corresponding to information about extracted ions such as mass or retention time) |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
137 - the data matrix (corresponding to related intensities) |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
138 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
139 **decimal places for [mass or retention time] values in identifiers** |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
140 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
141 | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time. |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
142 | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively. |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
143 | Theses parameters do not affect decimal places in columns other than the identifier one. |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
144 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
145 **Reported intensity values** |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
146 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
147 | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter: |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
148 | - into: integrated area of original (raw) peak |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
149 | - maxo: maximum intensity of original (raw) peak |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
150 | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’) |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
151 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
152 </token> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
153 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
154 <token name="@HELP_PEAKLIST_OUTPUT@"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
155 xset.variableMetadata.tsv : tabular format |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
156 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
157 | Table containing information about ions; can be used as one input of **Quality_Metrics** or **Generic_filter** modules. |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
158 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
159 xset.dataMatrix.tsv : tabular format |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
160 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
161 | Table containing ions' intensities; can be used as one input of **Quality_Metrics** or **Generic_filter** modules. |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
162 </token> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
163 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
164 <!-- CENTWAVE --> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
165 <token name="@COMMAND_CENTWAVE@"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
166 ppm $methods.ppm |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
167 peakwidth "c($methods.peakwidth)" |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
168 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
169 ## Advanced |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
170 snthresh $methods.CentWaveAdv.snthresh |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
171 prefilter "c($methods.CentWaveAdv.prefilter)" |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
172 mzCenterFun $methods.CentWaveAdv.mzCenterFun |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
173 integrate $methods.CentWaveAdv.integrate |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
174 mzdiff $methods.CentWaveAdv.mzdiff |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
175 fitgauss $methods.CentWaveAdv.fitgauss |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
176 noise $methods.CentWaveAdv.noise |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
177 verboseColumns $methods.CentWaveAdv.verboseColumns |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
178 </token> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
179 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
180 <xml name="input_centwave"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
181 <param argument="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="for the initial ROI definition." /> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
182 <param argument="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="with the expected approximate peak width in chromatographic space."> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
183 <expand macro="input_validator_range_float"/> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
184 </param> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
185 </xml> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
186 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
187 <xml name="input_centwaveAdv"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
188 <param argument="snthresh" type="integer" value="10" label="Signal to Noise ratio cutoff" /> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
189 <param argument="prefilter" type="text" value="3,100" label="Prefilter step for for the first analysis step (ROI detection)" help="Separate by coma k, I. Mass traces are only retained if they contain at least ‘k‘ peaks with intensity ‘>= I‘."> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
190 <expand macro="input_validator_range_integer"/> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
191 </param> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
192 <param argument="mzCenterFun" type="select" label="Name of the function to calculate the m/z center of the chromatographic peak" > |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
193 <option value="wMean">intensity weighted mean of the peak's m/z values</option> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
194 <option value="mean">mean of the peak's m/z values</option> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
195 <option value="apex">use the m/z value at the peak apex</option> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
196 <option value="wMeanApex3">ntensity weighted mean of the m/z value at the peak apex and the m/z values left and right of it</option> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
197 <option value="meanApex3">mean of the m/z value of the peak apex and the m/z values left and right of it</option> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
198 </param> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
199 <param argument="integrate" type="select" label="Integration method" > |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
200 <option value="1">peak limits are found through descent on the mexican hat filtered data (more robust, but less exact)</option> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
201 <option value="2">peak limits based on real data (more accurate but prone to noise)</option> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
202 </param> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
203 <param argument="mzdiff" type="float" value="-0.001" label="Minimum difference in m/z for peaks with overlapping retention times" help="can be negative to allow overlap" /> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
204 <param argument="fitgauss" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="fitgauss" help="whether or not a Gaussian should be fitted to each peak" /> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
205 <param argument="noise" type="integer" value="0" label="Noise filter" help="allowing to set a minimum intensity required for centroids to be considered in the first analysis step (centroids with intensity lower than ‘noise’ are omitted from ROI detection)." /> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
206 <param argument="verboseColumns" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="verbose Columns" help="whether additional peak meta data columns should be returned" /> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
207 </xml> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
208 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
209 <token name="@COMMAND_CENTWAVEADVROI@"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
210 #if $sectionROI.roiList: |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
211 roiList '$sectionROI.roiList' |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
212 firstBaselineCheck $sectionROI.firstBaselineCheck |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
213 #if $sectionROI.roiScales != "": |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
214 roiScales "c($sectionROI.roiScales)" |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
215 #end if |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
216 #end if |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
217 </token> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
218 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
219 <xml name="input_centwaveAdvROI" token_optional="true"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
220 <param argument="roiList" type="data" format="tabular" optional="@OPTIONAL@" label="List of regions-of-interest (ROI) representing detected mass traces" help="If ROIs are submitted the first analysis step is omitted and chromatographic peak detection is performed on the submitted ROIs. Each ROI is expected to have the following elements specified: ‘scmin’ (start scan index), ‘scmax’ (end scan index), ‘mzmin’ (minimum m/z), ‘mzmax’ (maximum m/z), ‘length’ (number of scans), ‘intensity’ (summed intensity)." /> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
221 <param argument="firstBaselineCheck" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Is continuous data within regions of interest is checked to be above the first baseline." /> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
222 <param argument="roiScales" type="text" value="" optional="true" label="Numeric vector defining the scale for each region of interest in ‘roiList’" help="Length equal to ‘roiList’ - Should be used for the centWave-wavelets (format 0.9,1,0.2)"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
223 <expand macro="input_validator_range_float"/> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
224 </param> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
225 </xml> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
226 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
227 <!-- MISC --> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
228 <token name="@HELP_AUTHORS@"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
229 .. class:: infomark |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
230 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
231 **Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
232 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
233 @HELP_AUTHORS_WRAPPERS@ |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
234 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
235 --------------------------------------------------- |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
236 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
237 </token> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
238 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
239 <token name="@HELP_XCMS_MANUAL@"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
240 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
241 For details and explanations concerning all the parameters and workflow of xcms_ package, see its manual_ and this example_ |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
242 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
243 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
244 .. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
245 .. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
246 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
247 </token> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
248 |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
249 <xml name="citation"> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
250 <citations> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
251 <citation type="doi">10.1021/ac051437y</citation> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
252 <expand macro="citation_w4m"/> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
253 </citations> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
254 </xml> |
|
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
|
255 </macros> |