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comparison semibin.xml @ 6:afee33334a63 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
author iuc
date Tue, 28 Oct 2025 08:18:37 +0000
parents fdb13ee4be38
children
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5:fdb13ee4be38 6:afee33334a63
43 #for $e in $mode.ref.taxonomy_annotation_table 43 #for $e in $mode.ref.taxonomy_annotation_table
44 '$e' 44 '$e'
45 #end for 45 #end for
46 #end if 46 #end if
47 #end if 47 #end if
48 --input-fasta 'contigs.fasta' 48 --input-fasta 'contigs.$input_fasta.ext'
49 #if $mode.select == "single": 49 #if $mode.select == "single":
50 --input-bam *.bam 50 --input-bam *.bam
51 #else: 51 #else:
52 #if $mode.align_select.align_select == "bam": 52 #if $mode.align_select.align_select == "bam":
53 --input-bam *.bam 53 --input-bam *.bam
172 </outputs> 172 </outputs>
173 <tests> 173 <tests>
174 <test expect_num_outputs="5"> 174 <test expect_num_outputs="5">
175 <conditional name="mode"> 175 <conditional name="mode">
176 <param name="select" value="single"/> 176 <param name="select" value="single"/>
177 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/> 177 <param name="input_fasta" ftype="fasta.gz" value="input_single.fasta.gz"/>
178 <param name="input_bam" ftype="bam" value="input_single.bam"/> 178 <param name="input_bam" ftype="bam" value="input_single.bam"/>
179 <conditional name="ref"> 179 <conditional name="ref">
180 <param name="select" value="taxonomy"/> 180 <param name="select" value="taxonomy"/>
181 <param name="taxonomy_annotation_table" value="taxonomy.tsv"/> 181 <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
182 </conditional> 182 </conditional>
223 </output> 223 </output>
224 </test> 224 </test>
225 <test expect_num_outputs="5"> 225 <test expect_num_outputs="5">
226 <conditional name="mode"> 226 <conditional name="mode">
227 <param name="select" value="single"/> 227 <param name="select" value="single"/>
228 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/> 228 <param name="input_fasta" ftype="fasta.bz2" value="input_single.fasta.bz2"/>
229 <param name="input_bam" ftype="bam" value="input_single.bam"/> 229 <param name="input_bam" ftype="bam" value="input_single.bam"/>
230 <conditional name="ref"> 230 <conditional name="ref">
231 <param name="select" value="ml"/> 231 <param name="select" value="ml"/>
232 </conditional> 232 </conditional>
233 <param name="environment" value="human_gut"/> 233 <param name="environment" value="human_gut"/>