Mercurial > repos > iuc > homer_findmotifsgenome

comparison homer_findMotifsGenome.xml @ 1:3126da33847c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
author iuc
date Sun, 26 Sep 2021 12:29:15 +0000
parents ec974e69e0b5
children a8f207b43f64
comparison
equal deleted inserted replaced
0:ec974e69e0b5 1:3126da33847c
56 #set sizee = int($genome.fixed_size.choose_center.sizes) + int($genome.fixed_size.size) 56 #set sizee = int($genome.fixed_size.choose_center.sizes) + int($genome.fixed_size.size)
57 -size '$genome.fixed_size.choose_center.sizes','${sizee}' 57 -size '$genome.fixed_size.choose_center.sizes','${sizee}'
58 #end if 58 #end if
59 #end if 59 #end if
60 #end if 60 #end if
61 #if str( $background.use ) != "none":
62 -bg '$background.bg'
63 #end if
64 #if str( $background.use ) == "withbg":
65 -keepOverlappingBg
66 #else if str( $background.use ) == "chopify":
67 -chopify
68 #end if
61 -len '$len' 69 -len '$len'
62 -S $S 70 -S $S
63 -mis $mis 71 -mis $mis
64 $norevopp 72 $norevopp
65 $nomotif 73 $nomotif
107 $advanced.homer12.quickMask 115 $advanced.homer12.quickMask
108 -minlp '$advanced.homer12.minlp' 116 -minlp '$advanced.homer12.minlp'
109 #elif str( $advanced.homer12.version ) == "homer1": 117 #elif str( $advanced.homer12.version ) == "homer1":
110 -depth '$advanced.homer12.depth' 118 -depth '$advanced.homer12.depth'
111 #end if 119 #end if
112 #if not $nomotif: 120 #if str( $background.use ) == "none":
113 && cp '${output}'/homerResults.html outputHomer.html 121 #if not $nomotif:
114 && cp -r '${output}' '${html_homer_file.files_path}' 122 && cp '${output}'/homerResults.html outputHomer.html
115 #end if 123 && cp -r '${output}' '${html_homer_file.files_path}'
116 #if not $motif_options.noknown: 124 #end if
117 && cp '${output}'/knownResults.html outputKnown.html 125 #if not $motif_options.noknown:
118 && cp -r '${output}' '${html_file.files_path}' 126 && cp '${output}'/knownResults.html outputKnown.html
127 && cp -r '${output}' '${html_file.files_path}'
128 #end if
129 #else
130 && cp '${output}'/homerResults.html outputHomer.html
131 && cp -r '${output}' '${html_homer_file.files_path}'
119 #end if 132 #end if
120 ]]></command> 133 ]]></command>
121 <inputs> 134 <inputs>
122 <param name="input" type="data" format="bed,encodepeak,tabular" label="Peak file"/> 135 <param name="input" type="data" format="bed,encodepeak,tabular" label="Peak file"/>
123 <conditional name="genome"> 136 <conditional name="genome">
146 <expand macro="mask_size"/> 159 <expand macro="mask_size"/>
147 </when> 160 </when>
148 <when value="history"> 161 <when value="history">
149 <param name="fasta" type="data" format="fasta" label="Select reference genome"/> 162 <param name="fasta" type="data" format="fasta" label="Select reference genome"/>
150 <expand macro="mask_size"/> 163 <expand macro="mask_size"/>
164 </when>
165 </conditional>
166 <conditional name="background">
167 <param name="use" type="select" label="Will you use a background model?" >
168 <option value="none" selected="true" >No background model</option>
169 <option value="model" >Background model with regions removed from target Peak file</option>
170 <option value="withbg" >Background model with regions not removed from target Peak file</option>
171 <option value="chopify" >Chop large background model regions to the average size of target Peak file regions</option>
172 </param>
173 <when value="none"></when>
174 <when value="model">
175 <param argument="-bg" type="data" format="bed,encodepeak,tabular" label="Background Peak file"/>
176 </when>
177 <when value="withbg">
178 <param argument="-bg" type="data" format="bed,encodepeak,tabular" label="Background Peak file"/>
179 </when>
180 <when value="chopify">
181 <param argument="-bg" type="data" format="bed,encodepeak,tabular" label="Background Peak file" />
151 </when> 182 </when>
152 </conditional> 183 </conditional>
153 <param argument="-len" type="text" value="8,10,12" label="comma-separated motif lengths" help="values greater 12 may cause the program to run out of memory - in these cases decrease the number of sequences analyzed (-N), or try analyzing shorter sequence regions (i.e. -size 100)"> 184 <param argument="-len" type="text" value="8,10,12" label="comma-separated motif lengths" help="values greater 12 may cause the program to run out of memory - in these cases decrease the number of sequences analyzed (-N), or try analyzing shorter sequence regions (i.e. -size 100)">
154 <validator type="regex" message="motif lengths must be comma-separated integers without space">^(\d+,)*(\d+)$</validator> 185 <validator type="regex" message="motif lengths must be comma-separated integers without space">^(\d+,)*(\d+)$</validator>
155 </param> 186 </param>
220 </section> 251 </section>
221 </inputs> 252 </inputs>
222 <outputs> 253 <outputs>
223 <data format="html" name="html_file" from_work_dir="outputKnown.html" label="${tool.name} on ${on_string}: Known motifs"> 254 <data format="html" name="html_file" from_work_dir="outputKnown.html" label="${tool.name} on ${on_string}: Known motifs">
224 <filter>motif_options['noknown'] is False</filter> 255 <filter>motif_options['noknown'] is False</filter>
256 <filter>background['use'] == "none"</filter>
225 </data> 257 </data>
226 <data format="html" name="html_homer_file" from_work_dir="outputHomer.html" label="${tool.name} on ${on_string}: De novo motifs"> 258 <data format="html" name="html_homer_file" from_work_dir="outputHomer.html" label="${tool.name} on ${on_string}: De novo motifs">
227 <filter>nomotif is False</filter> 259 <filter>nomotif is False</filter>
228 </data> 260 </data>
229 </outputs> 261 </outputs>
299 <output name="html_file"> 331 <output name="html_file">
300 <assert_contents> 332 <assert_contents>
301 <has_text text="CTCF_peaks_shifted_bed_motif - Homer Known Motif Enrichment Results"/> 333 <has_text text="CTCF_peaks_shifted_bed_motif - Homer Known Motif Enrichment Results"/>
302 <has_text text="Total Target Sequences = 40"/> 334 <has_text text="Total Target Sequences = 40"/>
303 <has_text text="RAP26"/> 335 <has_text text="RAP26"/>
336 </assert_contents>
337 </output>
338 </test>
339 <!-- background tests -->
340 <test expect_num_outputs="1">
341 <param name="input" value="fake_phix_peaks.bed"/>
342 <conditional name="genome">
343 <param name="source" value="installed"/>
344 <param name="all_fasta_source" value="phiX174"/>
345 </conditional>
346 <conditional name="background">
347 <param name="use" value="withbg" />
348 <param name="bg" value="fake_phix_peaks.subset.bed" />
349 </conditional>
350 <output name="html_homer_file">
351 <assert_contents>
352 <has_text text="HOXB13/MA0901.2/Jaspar(0.948)"/>
353 <has_text text="Yeast"/>
354 </assert_contents>
355 </output>
356 </test>
357 <test expect_num_outputs="1">
358 <param name="input" value="fake_phix_peaks.bed"/>
359 <conditional name="genome">
360 <param name="source" value="installed"/>
361 <param name="all_fasta_source" value="phiX174"/>
362 </conditional>
363 <conditional name="background">
364 <param name="use" value="chopify" />
365 <param name="bg" value="fake_phix_peaks.subset.bed" />
366 </conditional>
367 <output name="html_homer_file">
368 <assert_contents>
369 <has_text text="CCA"/>
370 <has_text text="YAP5"/>
304 </assert_contents> 371 </assert_contents>
305 </output> 372 </output>
306 </test> 373 </test>
307 </tests> 374 </tests>
308 <help><![CDATA[ 375 <help><![CDATA[