Mercurial > repos > galaxy-australia > cactus_cactus

comparison cactus_cactus.xml @ 13:9eeb13a92d79 draft

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planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2d431863824af49c82ff2ae318abee3b16141a4e
author galaxy-australia
date Wed, 05 Jul 2023 03:24:58 +0000
parents 2263989660f5
children 098506c54016
comparison
equal deleted inserted replaced
12:2263989660f5 13:9eeb13a92d79
22 22
23 ## Run cactus 23 ## Run cactus
24 24
25 #if $aln_mode.aln_mode_select == 'intraspecies': 25 #if $aln_mode.aln_mode_select == 'intraspecies':
26 ## Run cactus-pangenome 26 ## Run cactus-pangenome
27 ## --reference should be the first argument
28 ## https://github.com/ComparativeGenomicsToolkit/cactus/issues/1093#issuecomment-1620088688
27 cactus-pangenome 29 cactus-pangenome
30 --reference $aln_mode.ref_level
28 --binariesMode local 31 --binariesMode local
29 --maxCores \${GALAXY_SLOTS:-4} 32 --maxCores \${GALAXY_SLOTS:-4}
30 --maxMemory \${GALAXY_MEMORY_MB:-8192}M 33 --maxMemory \${GALAXY_MEMORY_MB:-8192}M
31 --outDir ./ 34 --outDir ./
32 --outName alignment 35 --outName alignment
33 --reference $aln_mode.ref_level 36 jobStore
34 ./jobStore
35 seqfile.txt 37 seqfile.txt
36 #else if $aln_mode.aln_mode_select == 'interspecies': 38 #else if $aln_mode.aln_mode_select == 'interspecies':
37 ## Run cactus normally 39 ## Run cactus normally
38 cactus 40 cactus
39 --binariesMode local 41 --binariesMode local
40 --maxCores \${GALAXY_SLOTS:-4} 42 --maxCores \${GALAXY_SLOTS:-4}
41 --maxMemory \${GALAXY_MEMORY_MB:-8192}M 43 --maxMemory \${GALAXY_MEMORY_MB:-8192}M
42 --workDir ./ 44 --workDir ./
43 jobStore 45 jobStore
44 seqfile.txt 46 seqfile.txt
45 alignment.full.hal 47 alignment.full.hal
175 <param name="label" value="pens_25"/> 177 <param name="label" value="pens_25"/>
176 <param name="fasta" value="pens_25.fasta.gz"/> 178 <param name="fasta" value="pens_25.fasta.gz"/>
177 </repeat> 179 </repeat>
178 <output name="out_hal"> 180 <output name="out_hal">
179 <assert_contents> 181 <assert_contents>
180 <has_size value="7420424" delta="200000" /> 182 <has_size value="6235006" delta="200000" />
181 </assert_contents> 183 </assert_contents>
182 </output> 184 </output>
183 <output name="out_gfa"> 185 <output name="out_gfa">
184 <assert_contents> 186 <assert_contents>
185 <has_size value="5786846" delta="200000" /> 187 <has_size value="5771414" delta="200000" />
186 </assert_contents> 188 </assert_contents>
187 </output> 189 </output>
188 </test> 190 </test>
189 <!-- FASTA header with spaces (used to fail) --> 191 <!-- FASTA header with spaces (used to fail) -->
190 <test expect_num_outputs="2"> 192 <test expect_num_outputs="2">