Mercurial > repos > galaxy-australia > cactus_cactus
comparison cactus_cactus.xml @ 2:8b67dd48fec1 draft
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 |
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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"> |