comparison macs2_callpeak.xml @ 19:86e2413cf3f8 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 7bd4238efae0d755b6a0dfff8daa43a228f18d96
author iuc
date Mon, 16 Oct 2023 13:18:37 +0000
parents 640d3af5d833
children
comparison
equal deleted inserted replaced
18:640d3af5d833 19:86e2413cf3f8
1 <tool id="macs2_callpeak" name="MACS2 callpeak" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> 1 <tool id="macs2_callpeak" name="MACS2 callpeak" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>Call peaks from alignment results</description> 2 <description>Call peaks from alignment results</description>
3 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>macs2_macros.xml</import> 4 <import>macs2_macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements"> 7 <expand macro="requirements">
8 </expand> 8 </expand>
9 <expand macro="stdio" /> 9 <expand macro="stdio" />
10 <expand macro="version_command" /> 10 <expand macro="version_command" />
11 <command><![CDATA[ 11 <command><![CDATA[
216 <option value="html">Summary page (html)</option> 216 <option value="html">Summary page (html)</option>
217 <option value="pdf">Plot in PDF (only available if a model is created and if BAMPE is not used)</option> 217 <option value="pdf">Plot in PDF (only available if a model is created and if BAMPE is not used)</option>
218 </param> 218 </param>
219 219
220 <section name="advanced_options" title="Advanced Options"> 220 <section name="advanced_options" title="Advanced Options">
221 <param name="to_large" argument="--to-large" type="boolean" truevalue="--to-large" falsevalue="" checked="false" 221 <param argument="--to-large" type="boolean" truevalue="--to-large" falsevalue="" checked="false"
222 label="When set, scale the small sample up to the bigger sample" 222 label="When set, scale the small sample up to the bigger sample"
223 help="By default, the bigger dataset will be scaled down towards the smaller dataset, which will lead to smaller p/qvalues and more specific results. Keep in mind that scaling down will bring down background noise more. Default: No"/> 223 help="By default, the bigger dataset will be scaled down towards the smaller dataset, which will lead to smaller p/qvalues and more specific results. Keep in mind that scaling down will bring down background noise more. Default: No"/>
224 <param argument="--nolambda" type="boolean" truevalue="--nolambda" falsevalue="" checked="false" 224 <param argument="--nolambda" type="boolean" truevalue="--nolambda" falsevalue="" checked="false"
225 label="Use fixed background lambda as local lambda for every peak region" help="up to 9X more time consuming. Default: No"/> 225 label="Use fixed background lambda as local lambda for every peak region" help="up to 9X more time consuming. Default: No"/>
226 <param name="spmr" argument="--SPMR" type="boolean" truevalue="--SPMR" falsevalue="" checked="false" 226 <param name="spmr" argument="--SPMR" type="boolean" truevalue="--SPMR" falsevalue="" checked="false"
242 <when value="broad"> 242 <when value="broad">
243 <param name="broad_cutoff" type="float" label="Cutoff for broad region" value="0.1" 243 <param name="broad_cutoff" type="float" label="Cutoff for broad region" value="0.1"
244 help="value is either p-value or q-value as specified above (--broad-cutoff)"/> 244 help="value is either p-value or q-value as specified above (--broad-cutoff)"/>
245 </when> 245 </when>
246 <when value="nobroad"> 246 <when value="nobroad">
247 <param name="call_summits" argument="--call-summits" type="boolean" truevalue="--call-summits" falsevalue="" checked="false" 247 <param argument="--call-summits" type="boolean" truevalue="--call-summits" falsevalue="" checked="false"
248 label="Use a more sophisticated signal processing approach to find subpeak summits in each enriched peak region"/> 248 label="Use a more sophisticated signal processing approach to find subpeak summits in each enriched peak region"/>
249 </when> 249 </when>
250 </conditional> 250 </conditional>
251 <expand macro="keep_duplicates" /> 251 <expand macro="keep_duplicates" />
252 <expand macro="fragment_size"/> 252 <expand macro="fragment_size"/>
311 <param name="qvalue" value="0.05"/> 311 <param name="qvalue" value="0.05"/>
312 <param name="band_width" value="300"/> 312 <param name="band_width" value="300"/>
313 <param name="outputs" value="peaks_tabular,bdg,html"/> 313 <param name="outputs" value="peaks_tabular,bdg,html"/>
314 <param name="effective_genome_size_options_selector" value="user_defined" /> 314 <param name="effective_genome_size_options_selector" value="user_defined" />
315 <param name="gsize" value="3300000000" /> 315 <param name="gsize" value="3300000000" />
316 <param name="lower" value="5" /> 316 <param name="mfold_lower" value="5" />
317 <param name="upper" value="50" /> 317 <param name="mfold_upper" value="50" />
318 <assert_command> 318 <assert_command>
319 <has_text text="--buffer-size"/> 319 <has_text text="--buffer-size"/>
320 <has_text text="--d-min"/> 320 <has_text text="--d-min"/>
321 </assert_command> 321 </assert_command>
322 <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg" lines_diff="1"/> 322 <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg" lines_diff="1"/>
338 <param name="qvalue" value="0.05"/> 338 <param name="qvalue" value="0.05"/>
339 <param name="band_width" value="300"/> 339 <param name="band_width" value="300"/>
340 <param name="outputs" value="pdf"/> 340 <param name="outputs" value="pdf"/>
341 <param name="effective_genome_size_options_selector" value="user_defined" /> 341 <param name="effective_genome_size_options_selector" value="user_defined" />
342 <param name="gsize" value="3300000000" /> 342 <param name="gsize" value="3300000000" />
343 <param name="lower" value="5" /> 343 <param name="mfold_lower" value="5" />
344 <param name="upper" value="50" /> 344 <param name="mfold_upper" value="50" />
345 <output name="output_plot" file="magic.pdf" compare="sim_size" ftype="pdf"/> 345 <output name="output_plot" file="magic.pdf" compare="sim_size" ftype="pdf"/>
346 </test> 346 </test>
347 <!-- Ensure BAMPE works --> 347 <!-- Ensure BAMPE works -->
348 <test expect_num_outputs="1"> 348 <test expect_num_outputs="1">
349 <param name="input_treatment_file" ftype="bam" value="bwa-mem-test1.bam"/> 349 <param name="input_treatment_file" ftype="bam" value="bwa-mem-test1.bam"/>