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comparison multigps.xml @ 47:7c3ef587aed9 draft

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Uploaded
author greg
date Tue, 21 Feb 2017 09:43:52 -0500
parents 9eb54f2ef321
children 6997a4b160c5
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46:9eb54f2ef321 47:7c3ef587aed9
24 --expt '$expt' 24 --expt '$expt'
25 --format $expt.ext 25 --format $expt.ext
26 #if str($ctrl) != 'None': 26 #if str($ctrl) != 'None':
27 --ctrl '$ctrl' 27 --ctrl '$ctrl'
28 #end if 28 #end if
29 #if str($verbose) == 'yes':
30 --verbose
31 #end if
32 --threads=\${GALAXY_SLOTS:-4} 29 --threads=\${GALAXY_SLOTS:-4}
33 --geninfo '$chromInfo' 30 --geninfo '$chromInfo'
34 ############################ 31 ############################
35 ## Advanced options 32 ## Advanced options
36 ############################ 33 ############################
175 <inputs> 172 <inputs>
176 <param name="expt" type="data" format="bam,bed,scidx" label="Run MultiGPS on"> 173 <param name="expt" type="data" format="bam,bed,scidx" label="Run MultiGPS on">
177 <validator type="unspecified_build" /> 174 <validator type="unspecified_build" />
178 </param> 175 </param>
179 <param name="ctrl" type="data" format="bam,bed,scidx" optional="True" label="Optional file containing reads from a control experiment" help="Must be same forat as the input above" /> 176 <param name="ctrl" type="data" format="bam,bed,scidx" optional="True" label="Optional file containing reads from a control experiment" help="Must be same forat as the input above" />
180 <param name="verbose" type="select" label="Generate intermediate files and extra output?" help="Verbose flag">
181 <option value="no" selected="True">No</option>
182 <option value="yes">Yes</option>
183 </param>
184 <!-- 177 <!--
185 ############################ 178 ############################
186 ## Advanced options 179 ## Advanced options
187 ############################ 180 ############################
188 --> 181 -->
405 </when> 398 </when>
406 </conditional> 399 </conditional>
407 </when> 400 </when>
408 <when value="hide" /> 401 <when value="hide" />
409 </conditional> 402 </conditional>
410 <!--
411 <param name="output_process_log" type="select" label="Output MultiGPS process log?">
412 <option value="no" selected="True">No</option>
413 <option value="yes">Yes</option>
414 </param>
415 -->
416 </inputs> 403 </inputs>
417 <outputs> 404 <outputs>
418 <data name="output_html" format="html" label="Results (HTML) on ${on_string}"/> 405 <data name="output_html" format="html" label="Results (HTML) on ${on_string}"/>
419 <data name="all_events_table" format="tabular" label="All events table on ${on_string}"/> 406 <data name="all_events_table" format="tabular" label="All events table on ${on_string}"/>
420 <data name="replicates_counts" format="tabular" label="Replicates counts on ${on_string}"/> 407 <data name="replicates_counts" format="tabular" label="Replicates counts on ${on_string}"/>
421 </outputs> 408 </outputs>
422 <tests> 409 <tests>
423 <test> 410 <test>
424 <param name="expt" value="expt_hg19.scidx" ftype="bam" dbkey="sacCer3" /> 411 <param name="expt" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
425 <param name="verbose" value="no" />
426 <param name="advanced_options_cond" value="hide" /> 412 <param name="advanced_options_cond" value="hide" />
427 <output name="output_html" file="hg19_output_html1.html" ftype="html" lines_diff="12"/> 413 <output name="output_html" file="hg19_output_html1.html" ftype="html" lines_diff="12"/>
428 <output name="all_events_table" file="hg19_all_events_table1.tabular" ftype="tabular"/> 414 <output name="all_events_table" file="hg19_all_events_table1.tabular" ftype="tabular"/>
429 <output name="replicates_counts" file="hg19_replicates_counts1.tabular" ftype="tabular"/> 415 <output name="replicates_counts" file="hg19_replicates_counts1.tabular" ftype="tabular"/>
430 </test> 416 </test>
431 <test> 417 <test>
432 <param name="expt" value="expt_hg19.scidx" ftype="bam" dbkey="sacCer3" /> 418 <param name="expt" value="expt_hg19.scidx" ftype="bam" dbkey="hg19" />
433 <param name="ctrl" value="cntrl_hg19.scidx" ftype="bam" dbkey="sacCer3" /> 419 <param name="ctrl" value="cntrl_hg19.scidx" ftype="bam" dbkey="hg19" />
434 <param name="verbose" value="no" />
435 <param name="advanced_options_cond" value="display" /> 420 <param name="advanced_options_cond" value="display" />
436 <output name="output_html" file="hg19_output_html2.html" ftype="html" lines_diff="12"/> 421 <output name="output_html" file="hg19_output_html2.html" ftype="html" lines_diff="12"/>
437 <output name="all_events_table" file="hg19_all_events_table2.tabular" ftype="tabular"/> 422 <output name="all_events_table" file="hg19_all_events_table2.tabular" ftype="tabular"/>
438 <output name="replicates_counts" file="hg19_replicates_counts2.tabular" ftype="tabular"/> 423 <output name="replicates_counts" file="hg19_replicates_counts2.tabular" ftype="tabular"/>
439 </test> 424 </test>
471 - **Window size for estimating scaling ratios** - Window size in base pairs for estimating scaling ratios 456 - **Window size for estimating scaling ratios** - Window size in base pairs for estimating scaling ratios
472 - **Plot diagnostic information for the chosen scaling method?** - Flag to plot diagnostic information for the chosen scaling method. 457 - **Plot diagnostic information for the chosen scaling method?** - Flag to plot diagnostic information for the chosen scaling method.
473 458
474 * **Running MultiGPS:** 459 * **Running MultiGPS:**
475 460
476 - **binding event read distribution file** - Binding event read distribution file for initializing models. The true distribution of reads around binding events is estimated during MultiGPS training. A default initial distribution appropriate for ChIP-seq data is used if this option is not specified. 461 - **Optional binding event read distribution file** - Binding event read distribution file for initializing models. The true distribution of reads around binding events is estimated during MultiGPS training. A default initial distribution appropriate for ChIP-seq data is used if this option is not specified.
477 - **Maximum number of training rounds for updating binding event read distributions** - Maximum number of training rounds for updating binding event read distributions. 462 - **Maximum number of training rounds for updating binding event read distributions** - Maximum number of training rounds for updating binding event read distributions.
478 - **Perform binding model updates?** - Perform binding model updates? 463 - **Perform binding model updates?** - Perform binding model updates?
479 - **Minimum number of events to support an update of the read distribution** - Minimum number of events to support an update of the read distribution 464 - **Minimum number of events to support an update of the read distribution** - Minimum number of events to support an update of the read distribution
480 - **Perform binding model smoothing?** - Smooth with a cubic spline using a specified smoothing factor. 465 - **Perform binding model smoothing?** - Smooth with a cubic spline using a specified smoothing factor.
481 - **Spline smoothing parameter** - Smoothing parameter for smoothing cubic spline. 466 - **Spline smoothing parameter** - Smoothing parameter for smoothing cubic spline.