Mercurial > repos > lecorguille > xcms_export_samplemetadata
annotate macros_xcms.xml @ 0:e3c06320f884 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
| author | lecorguille |
|---|---|
| date | Tue, 09 Oct 2018 12:50:47 -0400 |
| parents | |
| children | 8c62030a1136 |
| rev | line source |
|---|---|
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0
e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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1 <?xml version="1.0"?> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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2 <macros> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
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3 |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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4 <token name="@WRAPPER_VERSION@">3.0.0</token> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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5 <xml name="requirements"> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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6 <requirements> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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7 <requirement type="package" version="@WRAPPER_VERSION@">bioconductor-xcms</requirement> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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8 <requirement type="package" version="1.1_4">r-batch</requirement> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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9 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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10 <requirement type="package" version="6.0">unzip</requirement> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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11 <yield /> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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12 </requirements> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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13 </xml> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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14 |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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15 <!-- FILE_LOAD for planemo test --> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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16 <token name="@COMMAND_FILE_LOAD@"> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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17 #if $file_load_section.file_load_conditional.file_load_select == "yes": |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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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"): |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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changeset
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19 #set singlefile_galaxyPath = '|'.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] ) |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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20 #set singlefile_sampleName = '|'.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] ) |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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21 |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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changeset
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22 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName' |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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23 #else |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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24 zipfile '$file_load_section.file_load_conditional.input' |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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25 #end if |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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26 #end if |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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27 </token> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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28 |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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29 <xml name="input_file_load"> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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30 <section name="file_load_section" title="Resubmit your raw dataset or your zip file"> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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31 <conditional name="file_load_conditional"> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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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." > |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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changeset
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33 <option value="no" >no need</option> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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changeset
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34 <option value="yes" >yes</option> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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35 </param> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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36 <when value="no"> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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37 </when> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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38 <when value="yes"> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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changeset
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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." /> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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40 </when> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
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41 </conditional> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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changeset
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42 </section> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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43 </xml> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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44 |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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45 <xml name="test_file_load_zip"> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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46 <section name="file_load_section"> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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47 <conditional name="file_load_conditional"> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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48 <param name="file_load_select" value="yes" /> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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49 <param name="input" value="faahKO_reduce.zip" ftype="zip" /> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
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50 </conditional> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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51 </section> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
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52 </xml> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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53 |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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54 <xml name="test_file_load_zip_sacuri"> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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55 <section name="file_load_section"> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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56 <conditional name="file_load_conditional"> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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57 <param name="file_load_select" value="yes" /> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
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58 <param name="input" value="sacuri_dir_root.zip" ftype="zip" /> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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59 </conditional> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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60 </section> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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61 </xml> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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62 |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
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63 <xml name="test_file_load_single"> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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64 <section name="file_load_section"> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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65 <conditional name="file_load_conditional"> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
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66 <param name="file_load_select" value="yes" /> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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67 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" /> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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68 </conditional> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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69 </section> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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70 </xml> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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71 |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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72 <xml name="test_file_load_single_ko15"> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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changeset
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73 <section name="file_load_section"> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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74 <conditional name="file_load_conditional"> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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75 <param name="file_load_select" value="yes" /> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
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76 <param name="input" value="ko15.CDF" ftype="netcdf" /> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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77 </conditional> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
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78 </section> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
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79 </xml> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
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80 |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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81 <!-- PEAKLIST --> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
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82 <token name="@COMMAND_PEAKLIST@"> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
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83 #if $peaklist.peaklistBool |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
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84 convertRTMinute $peaklist.convertRTMinute |
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85 numDigitsMZ $peaklist.numDigitsMZ |
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86 numDigitsRT $peaklist.numDigitsRT |
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87 intval $peaklist.intval |
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88 naTOzero $peaklist.naTOzero |
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89 #end if |
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90 </token> |
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91 |
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92 <xml name="input_peaklist"> |
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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"/> |
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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" /> |
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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" /> |
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96 <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below"> |
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97 <option value="into" selected="true">into</option> |
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98 <option value="maxo">maxo</option> |
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99 <option value="intb">intb</option> |
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100 </param> |
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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"/> |
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102 </xml> |
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103 |
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104 <xml name="input_peaklist_section"> |
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105 <section name="peaklist" title="Peak List" expanded="True"> |
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106 <param name="peaklistBool" type="hidden" label="Get the Peak List" value="True" /> |
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107 <expand macro="input_peaklist"/> |
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108 </section> |
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109 </xml> |
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110 |
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111 <xml name="input_peaklist_conditional"> |
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112 <conditional name="peaklist"> |
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113 <param name="peaklistBool" type="boolean" label="Get the Peak List" /> |
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114 <when value="true"> |
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115 <expand macro="input_peaklist"/> |
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116 </when> |
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117 <when value="false" /> |
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118 </conditional> |
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119 </xml> |
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120 |
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121 <xml name="output_peaklist" token_function=""> |
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122 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" > |
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123 <filter>(peaklist['peaklistBool'])</filter> |
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124 </data> |
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125 <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" from_work_dir="dataMatrix.tsv" > |
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126 <filter>(peaklist['peaklistBool'])</filter> |
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127 </data> |
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128 </xml> |
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129 |
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130 <token name="@HELP_PEAKLIST@"> |
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131 |
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132 Get a Peak List |
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133 --------------- |
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134 |
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135 If 'true', the module generates two additional files corresponding to the peak list: |
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136 - the variable metadata file (corresponding to information about extracted ions such as mass or retention time) |
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137 - the data matrix (corresponding to related intensities) |
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138 |
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139 **decimal places for [mass or retention time] values in identifiers** |
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140 |
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141 | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time. |
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142 | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively. |
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143 | Theses parameters do not affect decimal places in columns other than the identifier one. |
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144 |
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145 **Reported intensity values** |
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146 |
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147 | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter: |
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148 | - into: integrated area of original (raw) peak |
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149 | - maxo: maximum intensity of original (raw) peak |
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150 | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’) |
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151 |
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152 </token> |
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153 |
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154 <token name="@HELP_PEAKLIST_OUTPUT@"> |
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155 xset.variableMetadata.tsv : tabular format |
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156 |
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157 | Table containing information about ions; can be used as one input of **Quality_Metrics** or **Generic_filter** modules. |
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158 |
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159 xset.dataMatrix.tsv : tabular format |
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160 |
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161 | Table containing ions' intensities; can be used as one input of **Quality_Metrics** or **Generic_filter** modules. |
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162 </token> |
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163 |
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164 <!-- CENTWAVE --> |
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165 <token name="@COMMAND_CENTWAVE@"> |
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166 ppm $methods.ppm |
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167 peakwidth "c($methods.peakwidth)" |
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168 |
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169 ## Advanced |
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170 snthresh $methods.CentWaveAdv.snthresh |
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171 prefilter "c($methods.CentWaveAdv.prefilter)" |
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172 mzCenterFun $methods.CentWaveAdv.mzCenterFun |
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173 integrate $methods.CentWaveAdv.integrate |
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174 mzdiff $methods.CentWaveAdv.mzdiff |
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175 fitgauss $methods.CentWaveAdv.fitgauss |
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176 noise $methods.CentWaveAdv.noise |
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177 verboseColumns $methods.CentWaveAdv.verboseColumns |
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178 </token> |
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179 |
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180 <xml name="input_centwave"> |
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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." /> |
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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."> |
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183 <expand macro="input_validator_range_float"/> |
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184 </param> |
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185 </xml> |
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186 |
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187 <xml name="input_centwaveAdv"> |
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188 <param argument="snthresh" type="integer" value="10" label="Signal to Noise ratio cutoff" /> |
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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‘."> |
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190 <expand macro="input_validator_range_integer"/> |
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191 </param> |
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192 <param argument="mzCenterFun" type="select" label="Name of the function to calculate the m/z center of the chromatographic peak" > |
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193 <option value="wMean">intensity weighted mean of the peak's m/z values</option> |
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194 <option value="mean">mean of the peak's m/z values</option> |
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195 <option value="apex">use the m/z value at the peak apex</option> |
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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> |
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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> |
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198 </param> |
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199 <param argument="integrate" type="select" label="Integration method" > |
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200 <option value="1">peak limits are found through descent on the mexican hat filtered data (more robust, but less exact)</option> |
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201 <option value="2">peak limits based on real data (more accurate but prone to noise)</option> |
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202 </param> |
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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" /> |
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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" /> |
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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)." /> |
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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" /> |
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207 </xml> |
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208 |
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209 <token name="@COMMAND_CENTWAVEADVROI@"> |
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210 #if $sectionROI.roiList: |
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211 roiList '$sectionROI.roiList' |
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212 firstBaselineCheck $sectionROI.firstBaselineCheck |
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213 #if $sectionROI.roiScales != "": |
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214 roiScales "c($sectionROI.roiScales)" |
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215 #end if |
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216 #end if |
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217 </token> |
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218 |
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219 <xml name="input_centwaveAdvROI" token_optional="true"> |
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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)." /> |
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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." /> |
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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)"> |
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223 <expand macro="input_validator_range_float"/> |
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224 </param> |
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225 </xml> |
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226 |
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227 <!-- MISC --> |
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228 <token name="@HELP_AUTHORS@"> |
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229 .. class:: infomark |
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230 |
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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 |
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232 |
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233 @HELP_AUTHORS_WRAPPERS@ |
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234 |
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235 --------------------------------------------------- |
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236 |
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237 </token> |
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238 |
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239 <token name="@HELP_XCMS_MANUAL@"> |
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240 |
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241 For details and explanations concerning all the parameters and workflow of xcms_ package, see its manual_ and this example_ |
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242 |
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243 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html |
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244 .. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf |
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245 .. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html |
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246 |
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247 </token> |
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248 |
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249 <xml name="citation"> |
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250 <citations> |
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251 <citation type="doi">10.1021/ac051437y</citation> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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252 <expand macro="citation_w4m"/> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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253 </citations> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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changeset
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254 </xml> |
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e3c06320f884
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff
changeset
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255 </macros> |