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comparison macs2_callpeak.xml @ 63:25e46cf1ee36 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
author iuc
date Sat, 02 Apr 2022 21:36:50 +0000
parents 1ac88e46ee0f
children
comparison
equal deleted inserted replaced
62:1ac88e46ee0f 63:25e46cf1ee36
1 <tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.6" profile="17.09"> 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"/> 3 <expand macro="bio_tools"/>
4 <macros> 4 <macros>
5 <import>macs2_macros.xml</import> 5 <import>macs2_macros.xml</import>
6 </macros> 6 </macros>
71 --keep-dup '${ advanced_options.keep_dup_options.user_keepdup }' 71 --keep-dup '${ advanced_options.keep_dup_options.user_keepdup }'
72 #else 72 #else
73 --keep-dup '${ advanced_options.keep_dup_options.keep_dup_options_selector }' 73 --keep-dup '${ advanced_options.keep_dup_options.keep_dup_options_selector }'
74 #end if 74 #end if
75 75
76 --d-min $advanced_options.d_min
77 --buffer-size $advanced_options.buffer_size
76 78
77 ## With --bdg two additional output files will be generated. 79 ## With --bdg two additional output files will be generated.
78 #if "bdg" in str($outputs).split(','): 80 #if "bdg" in str($outputs).split(','):
79 --bdg 81 --bdg
80 #end if 82 #end if
245 <param name="call_summits" argument="--call-summits" type="boolean" truevalue="--call-summits" falsevalue="" checked="false" 247 <param name="call_summits" argument="--call-summits" type="boolean" truevalue="--call-summits" falsevalue="" checked="false"
246 label="Use a more sophisticated signal processing approach to find subpeak summits in each enriched peak region"/> 248 label="Use a more sophisticated signal processing approach to find subpeak summits in each enriched peak region"/>
247 </when> 249 </when>
248 </conditional> 250 </conditional>
249 <expand macro="keep_duplicates" /> 251 <expand macro="keep_duplicates" />
252 <expand macro="fragment_size"/>
253 <expand macro="buffer_size"/>
250 </section> 254 </section>
251 </inputs> 255 </inputs>
252 <outputs> 256 <outputs>
253 <!--callpeaks output--> 257 <!--callpeaks output-->
254 <data name="output_tabular" format="tabular" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Peaks in tabular format)"> 258 <data name="output_tabular" format="tabular" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Peaks in tabular format)">
309 <param name="outputs" value="peaks_tabular,bdg,html"/> 313 <param name="outputs" value="peaks_tabular,bdg,html"/>
310 <param name="effective_genome_size_options_selector" value="user_defined" /> 314 <param name="effective_genome_size_options_selector" value="user_defined" />
311 <param name="gsize" value="3300000000" /> 315 <param name="gsize" value="3300000000" />
312 <param name="lower" value="5" /> 316 <param name="lower" value="5" />
313 <param name="upper" value="50" /> 317 <param name="upper" value="50" />
318 <assert_command>
319 <has_text text="--buffer-size"/>
320 <has_text text="--d-min"/>
321 </assert_command>
314 <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"/>
315 <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg" lines_diff="1"/> 323 <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg" lines_diff="1"/>
316 <output name="output_tabular" compare="contains" file="callpeak_part.tabular" lines_diff="3"/> 324 <output name="output_tabular" compare="contains" file="callpeak_part.tabular" lines_diff="3"/>
317 <output name="output_extra_files"> 325 <output name="output_extra_files">
318 <assert_contents> 326 <assert_contents>
332 <param name="outputs" value="pdf"/> 340 <param name="outputs" value="pdf"/>
333 <param name="effective_genome_size_options_selector" value="user_defined" /> 341 <param name="effective_genome_size_options_selector" value="user_defined" />
334 <param name="gsize" value="3300000000" /> 342 <param name="gsize" value="3300000000" />
335 <param name="lower" value="5" /> 343 <param name="lower" value="5" />
336 <param name="upper" value="50" /> 344 <param name="upper" value="50" />
337 <output name="output_plot" file="magic.pdf" ftype="pdf" compare="contains" /> 345 <output name="output_plot" file="magic.pdf" compare="sim_size" ftype="pdf"/>
338 </test> 346 </test>
339 <!-- Ensure BAMPE works --> 347 <!-- Ensure BAMPE works -->
340 <test expect_num_outputs="1"> 348 <test expect_num_outputs="1">
341 <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"/>
342 <param name="format" value="BAMPE" /> 350 <param name="format" value="BAMPE" />