Mercurial > repos > galaxy-australia > cactus_cactus

comparison cactus_cactus.xml @ 2:8b67dd48fec1 draft

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planemo upload for repository https://github.com/usegalaxy-au/tools-au commit b2235e7e7970f74e5d55ce150e3380d93fcdd70f
author galaxy-australia
date Tue, 13 Sep 2022 00:17:17 +0000
parents 1bc1199f0ff4
children 9422c5a87ee2
comparison
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1:1bc1199f0ff4 2:8b67dd48fec1
65 ./jobStore 65 ./jobStore
66 ./seqfile.txt 66 ./seqfile.txt
67 pangenome.paf 67 pangenome.paf
68 alignment.hal 68 alignment.hal
69 --pangenome 69 --pangenome
70 --pafInput
71 --binariesMode local 70 --binariesMode local
72 --workDir ./ 71 --workDir ./
73 #else if $aln_mode.aln_mode_select == 'interspecies': 72 #else if $aln_mode.aln_mode_select == 'interspecies':
74 ## Run cactus normally 73 ## Run cactus normally
75 cactus 74 cactus
131 <param name="label" value="simRat_chr6"/> 130 <param name="label" value="simRat_chr6"/>
132 <param name="fasta" value="simRat_chr6.fasta"/> 131 <param name="fasta" value="simRat_chr6.fasta"/>
133 </repeat> 132 </repeat>
134 <output name="out_hal"> 133 <output name="out_hal">
135 <assert_contents> 134 <assert_contents>
136 <has_size value="5272354" delta="200000" /> 135 <has_size value="4783905" delta="200000" />
137 </assert_contents> 136 </assert_contents>
138 </output> 137 </output>
139 </test> 138 </test>
140 <!-- within-species mode --> 139 <!-- within-species mode -->
141 <test expect_num_outputs="1"> 140 <test expect_num_outputs="1">
162 <param name="label" value="simRat_chr6"/> 161 <param name="label" value="simRat_chr6"/>
163 <param name="fasta" value="simRat_chr6.fasta"/> 162 <param name="fasta" value="simRat_chr6.fasta"/>
164 </repeat> 163 </repeat>
165 <output name="out_hal"> 164 <output name="out_hal">
166 <assert_contents> 165 <assert_contents>
167 <has_size value="2119332" delta="200000" /> 166 <has_size value="1349620" delta="200000" />
168 </assert_contents> 167 </assert_contents>
169 </output> 168 </output>
170 </test> 169 </test>
171 <!-- compressed input --> 170 <!-- compressed input -->
172 <test expect_num_outputs="1"> 171 <test expect_num_outputs="1">
185 <param name="label" value="pens_25"/> 184 <param name="label" value="pens_25"/>
186 <param name="fasta" value="pens_25.fasta.gz"/> 185 <param name="fasta" value="pens_25.fasta.gz"/>
187 </repeat> 186 </repeat>
188 <output name="out_hal"> 187 <output name="out_hal">
189 <assert_contents> 188 <assert_contents>
190 <has_size value="8382049" delta="200000" /> 189 <has_size value="7420424" delta="200000" />
191 </assert_contents> 190 </assert_contents>
192 </output> 191 </output>
193 </test> 192 </test>
194 <!-- FASTA header --> 193 <!-- FASTA header -->
195 <test expect_exit_code="1" expect_failure="true"> 194 <test expect_exit_code="1" expect_failure="true">