Mercurial > repos > galaxyp > openms
comparison OpenSwathWorkflow.xml @ 4:60a33af52042 draft default tip
Uploaded
| author | galaxyp |
|---|---|
| date | Wed, 13 May 2015 21:19:44 -0400 |
| parents | 3070d71e0e5c |
| children |
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| 3:75537a09e9fa | 4:60a33af52042 |
|---|---|
| 25 #end if | 25 #end if |
| 26 #end if | 26 #end if |
| 27 #if $param_tr_irt: | 27 #if $param_tr_irt: |
| 28 -tr_irt $param_tr_irt | 28 -tr_irt $param_tr_irt |
| 29 #end if | 29 #end if |
| 30 #if $param_out_features: | 30 #if $output_fmt == 'tsv': |
| 31 -out_features $param_out_features | 31 -out_tsv "$out_tsv" |
| 32 #end if | 32 #else: |
| 33 #if $param_out_tsv: | 33 -out_features "$out_features" |
| 34 -out_tsv "$param_out_tsv" | |
| 35 #end if | 34 #end if |
| 36 #if $param_out_chrom: | 35 #if $param_out_chrom: |
| 37 -out_chrom $param_out_chrom | 36 -out_chrom $param_out_chrom |
| 38 #end if | 37 #end if |
| 39 #if $param_rt_extraction_window: | 38 #if $param_rt_extraction_window: |
| 237 <option value="traML">traML</option> | 236 <option value="traML">traML</option> |
| 238 <option value="tsv">tsv</option> | 237 <option value="tsv">tsv</option> |
| 239 <option value="csv">csv</option> | 238 <option value="csv">csv</option> |
| 240 </param> | 239 </param> |
| 241 <param name="param_tr_irt" type="data" format="traml" optional="True" label="transition file ('TraML')" help="(-tr_irt) "/> | 240 <param name="param_tr_irt" type="data" format="traml" optional="True" label="transition file ('TraML')" help="(-tr_irt) "/> |
| 242 <param name="param_out_tsv" type="text" size="30" label="TSV output file (mProphet compatible)" help="(-out_tsv) "> | 241 <param name="output_fmt" type="select" label="Select feature list output format"> |
| 243 <sanitizer> | 242 <option value="featurexml">FeatureXML</option> |
| 244 <valid initial="string.printable"> | 243 <option value="tsv">TSV output file (mProphet compatible)</option> |
| 245 <remove value="'"/> | |
| 246 <remove value="""/> | |
| 247 </valid> | |
| 248 </sanitizer> | |
| 249 </param> | 244 </param> |
| 250 <param name="param_rt_extraction_window" type="float" value="600.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 600 means to extract around +/- 300 s of the expected elution)" help="(-rt_extraction_window) "/> | 245 <param name="param_rt_extraction_window" type="float" value="600.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 600 means to extract around +/- 300 s of the expected elution)" help="(-rt_extraction_window) "/> |
| 251 <param name="param_mz_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="Extraction window used (in Thomson, to use ppm see -ppm flag)" help="(-mz_extraction_window) "/> | 246 <param name="param_mz_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="Extraction window used (in Thomson, to use ppm see -ppm flag)" help="(-mz_extraction_window) "/> |
| 252 <param name="param_ppm" type="boolean" truevalue="-ppm" falsevalue="" checked="false" optional="True" label="m/z extraction_window is in ppm" help="(-ppm) "/> | 247 <param name="param_ppm" type="boolean" truevalue="-ppm" falsevalue="" checked="false" optional="True" label="m/z extraction_window is in ppm" help="(-ppm) "/> |
| 253 <param name="param_Scoring_stop_report_after_feature" type="integer" value="-1" label="Stop reporting after feature (ordered by quality; -1 means do not stop)" help="(-stop_report_after_feature) "/> | 248 <param name="param_Scoring_stop_report_after_feature" type="integer" value="-1" label="Stop reporting after feature (ordered by quality; -1 means do not stop)" help="(-stop_report_after_feature) "/> |
| 343 <param name="param_Scoring_Scores_use_ms1_correlation" type="boolean" truevalue="-Scoring:Scores:use_ms1_correlation" falsevalue="" checked="false" optional="True" label="Use the correlation scores with the MS1 elution profiles" help="(-use_ms1_correlation) "/> | 338 <param name="param_Scoring_Scores_use_ms1_correlation" type="boolean" truevalue="-Scoring:Scores:use_ms1_correlation" falsevalue="" checked="false" optional="True" label="Use the correlation scores with the MS1 elution profiles" help="(-use_ms1_correlation) "/> |
| 344 <param name="param_Scoring_Scores_use_ms1_fullscan" type="boolean" truevalue="-Scoring:Scores:use_ms1_fullscan" falsevalue="" checked="false" optional="True" label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" help="(-use_ms1_fullscan) "/> | 339 <param name="param_Scoring_Scores_use_ms1_fullscan" type="boolean" truevalue="-Scoring:Scores:use_ms1_fullscan" falsevalue="" checked="false" optional="True" label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" help="(-use_ms1_fullscan) "/> |
| 345 </expand> | 340 </expand> |
| 346 </inputs> | 341 </inputs> |
| 347 <outputs> | 342 <outputs> |
| 348 <data name="param_out_features" format="featurexml"/> | 343 <data name="out_features" format="featurexml"> |
| 344 <filter>output_fmt == 'featurexml'</filter> | |
| 345 </data> | |
| 346 <data name="out_tsv" format="tabular"> | |
| 347 <filter>output_fmt == 'tsv'</filter> | |
| 348 </data> | |
| 349 <data name="param_out_chrom" format="mzml"/> | 349 <data name="param_out_chrom" format="mzml"/> |
| 350 </outputs> | 350 </outputs> |
| 351 <help>**What it does** | 351 <help>**What it does** |
| 352 | 352 |
| 353 Complete workflow to run OpenSWATH | 353 Complete workflow to run OpenSWATH |