Mercurial > repos > iuc > macs2
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 |
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date | Mon, 16 Oct 2023 13:18:37 +0000 |
parents | 640d3af5d833 |
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18:640d3af5d833 | 19:86e2413cf3f8 |
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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"/> |