Mercurial > repos > iuc > meme_fimo

comparison fimo.xml @ 15:0c5239d1aa65 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
author iuc
date Wed, 11 Dec 2019 18:05:35 -0500
parents c1a9a297ba8b
children be146697a083
comparison
equal deleted inserted replaced
14:c1a9a297ba8b 15:0c5239d1aa65
45 '${fasta_type.input_database}' 45 '${fasta_type.input_database}'
46 #else: 46 #else:
47 '${fasta_type.input_database.fields.path}' 47 '${fasta_type.input_database.fields.path}'
48 #end if 48 #end if
49 && mv ./out/fimo.html '${html_outfile}' 49 && mv ./out/fimo.html '${html_outfile}'
50 && mv ./out/fimo.txt '${txt_outfile}' 50 && mv ./out/fimo.tsv '${txt_outfile}'
51 && mv ./out/fimo.xml '${xml_outfile}' 51 && mv ./out/fimo.xml '${xml_outfile}'
52 && mv ./out/fimo.gff '${gff_outfile}' 52 && mv ./out/fimo.gff '${gff_outfile}'
53 ]]></command> 53 ]]></command>
54 <inputs> 54 <inputs>
55 <param name="input_motifs" type="data" format="memexml" label="DREME or MEME output XML file" 55 <param name="input_motifs" type="data" format="memexml" label="DREME or MEME output XML file"
233 <param name="options_type_selector" value="basic"/> 233 <param name="options_type_selector" value="basic"/>
234 <param name="html_outfile" value="True"/> 234 <param name="html_outfile" value="True"/>
235 <param name="xml_outfile" value="True"/> 235 <param name="xml_outfile" value="True"/>
236 <param name="gff_outfile" value="True"/> 236 <param name="gff_outfile" value="True"/>
237 <param name="non_commercial_use" value="True"/> 237 <param name="non_commercial_use" value="True"/>
238 <output name="html_outfile" file="fimo_output_test1.html" lines_diff="20"/> 238 <output name="html_outfile" file="fimo_output_test1.html" compare="contains"/>
239 <output name="txt_outfile" file="fimo_output_test1.txt"/> 239 <output name="txt_outfile" file="fimo_output_test1.txt" compare="contains"/>
240 <output name="xml_outfile" file="fimo_output_test1.xml" lines_diff="20"/> 240 <output name="xml_outfile" file="fimo_output_test1.xml" compare="contains"/>
241 <output name="gff_outfile" file="fimo_output_test1.gff"/> 241 <output name="gff_outfile" file="fimo_output_test1.gff" compare="contains"/>
242 </test> 242 </test>
243 <test expect_num_outputs="4"> 243 <test expect_num_outputs="4">
244 <param name="input_motifs" value="dreme_fimo_input_1.xml" ftype="memexml"/> 244 <param name="input_motifs" value="dreme_fimo_input_1.xml" ftype="memexml"/>
245 <param name="fasta_type_selector" value="history"/> 245 <param name="fasta_type_selector" value="history"/>
246 <param name="input_database" value="hsa_chrM.fa" ftype="fasta"/> 246 <param name="input_database" value="hsa_chrM.fa" ftype="fasta"/>
250 <param name="bgfile" value="fimo_background_probs_hsa_chrM.txt"/> 250 <param name="bgfile" value="fimo_background_probs_hsa_chrM.txt"/>
251 <param name="html_outfile" value="True"/> 251 <param name="html_outfile" value="True"/>
252 <param name="xml_outfile" value="True"/> 252 <param name="xml_outfile" value="True"/>
253 <param name="gff_outfile" value="True"/> 253 <param name="gff_outfile" value="True"/>
254 <param name="non_commercial_use" value="True"/> 254 <param name="non_commercial_use" value="True"/>
255 <output name="html_outfile" file="fimo_output_test2.html" lines_diff="20"/> 255 <output name="html_outfile" file="fimo_output_test2.html" compare="contains"/>
256 <output name="txt_outfile" file="fimo_output_test2.txt"/> 256 <output name="txt_outfile" file="fimo_output_test2.txt" compare="contains"/>
257 <output name="xml_outfile" file="fimo_output_test2.xml" lines_diff="20"/> 257 <output name="xml_outfile" file="fimo_output_test2.xml" compare="contains"/>
258 <output name="gff_outfile" file="fimo_output_test2.gff"/> 258 <output name="gff_outfile" file="fimo_output_test2.gff" compare="contains"/>
259 </test> 259 </test>
260 <test expect_num_outputs="3"> 260 <test expect_num_outputs="3">
261 <param name="input_motifs" value="dreme_fimo_input_1.xml" ftype="memexml"/> 261 <param name="input_motifs" value="dreme_fimo_input_1.xml" ftype="memexml"/>
262 <param name="fasta_type_selector" value="history"/> 262 <param name="fasta_type_selector" value="history"/>
263 <param name="input_database" value="hsa_chrM.fa" ftype="fasta"/> 263 <param name="input_database" value="hsa_chrM.fa" ftype="fasta"/>
271 </repeat> 271 </repeat>
272 <param name="html_outfile" value="True"/> 272 <param name="html_outfile" value="True"/>
273 <param name="xml_outfile" value="True"/> 273 <param name="xml_outfile" value="True"/>
274 <param name="gff_outfile" value="False"/> 274 <param name="gff_outfile" value="False"/>
275 <param name="non_commercial_use" value="True"/> 275 <param name="non_commercial_use" value="True"/>
276 <output name="html_outfile" file="fimo_output_test3.html" lines_diff="20"/> 276 <output name="html_outfile" file="fimo_output_test3.html" compare="contains"/>
277 <output name="txt_outfile" file="fimo_output_test3.txt"/> 277 <output name="txt_outfile" file="fimo_output_test3.txt" compare="contains"/>
278 <output name="xml_outfile" file="fimo_output_test3.xml" lines_diff="20"/> 278 <output name="xml_outfile" file="fimo_output_test3.xml" compare="contains"/>
279 </test> 279 </test>
280 </tests> 280 </tests>
281 <help> 281 <help>
282 282
283 .. class:: warningmark 283 .. class:: warningmark