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comparison OpenSwathWorkflow.xml @ 4:60a33af52042 draft default tip

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author galaxyp
date Wed, 13 May 2015 21:19:44 -0400
parents 3070d71e0e5c
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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="&quot;"/>
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