Mercurial > repos > galaxy-australia > cactus_cactus

comparison cactus_cactus.xml @ 12:2263989660f5 draft

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planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cb75f42cdcae1a92023e6e5b33a8a260877d76fe
author galaxy-australia
date Mon, 15 May 2023 04:34:02 +0000
parents 6ae5a7b5a0a2
children 9eeb13a92d79
comparison
equal deleted inserted replaced
11:bdfbaf0c10aa 12:2263989660f5
21 #end for 21 #end for
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 ## If we're doing a pangenome, we need to run the steps manually 26 ## Run cactus-pangenome
27 cactus-minigraph 27 cactus-pangenome
28 --binariesMode local
29 --mapCores \${GALAXY_SLOTS:-4}
30 --maxMemory \${GALAXY_MEMORY_MB:-8192}M
31 --reference $aln_mode.ref_level
32 --workDir ./
33 ./jobStore
34 ./seqfile.txt
35 pangenome.gfa
36 &&
37 cactus-graphmap
38 --binariesMode local 28 --binariesMode local
39 --maxCores \${GALAXY_SLOTS:-4} 29 --maxCores \${GALAXY_SLOTS:-4}
40 --maxMemory \${GALAXY_MEMORY_MB:-8192}M 30 --maxMemory \${GALAXY_MEMORY_MB:-8192}M
41 --outputFasta pangenome.gfa.fa 31 --outDir ./
42 --reference $aln_mode.ref_level
43 --workDir ./
44 ./jobStore
45 ./seqfile.txt
46 pangenome.gfa
47 pangenome.paf
48 &&
49 cactus-align
50 --binariesMode local
51 --maxCores \${GALAXY_SLOTS:-4}
52 --maxMemory \${GALAXY_MEMORY_MB:-8192}M
53 --outVG
54 --pangenome
55 --reference $aln_mode.ref_level
56 --workDir ./
57 ./jobStore
58 ./seqfile.txt
59 pangenome.paf
60 alignment.hal
61 &&
62 cactus-graphmap-join
63 --binariesMode local
64 --giraffe
65 --maxCores \${GALAXY_SLOTS:-4}
66 --maxMemory \${GALAXY_MEMORY_MB:-8192}M
67 --outName alignment 32 --outName alignment
68 --reference $aln_mode.ref_level 33 --reference $aln_mode.ref_level
69 --vg alignment.vg
70 --outDir ./
71 ./jobStore 34 ./jobStore
35 seqfile.txt
72 #else if $aln_mode.aln_mode_select == 'interspecies': 36 #else if $aln_mode.aln_mode_select == 'interspecies':
73 ## Run cactus normally 37 ## Run cactus normally
74 cactus 38 cactus
75 --binariesMode local 39 --binariesMode local
76 --maxCores \${GALAXY_SLOTS:-4} 40 --maxCores \${GALAXY_SLOTS:-4}
77 --maxMemory \${GALAXY_MEMORY_MB:-8192}M 41 --maxMemory \${GALAXY_MEMORY_MB:-8192}M
78 --workDir ./ 42 --workDir ./
79 jobStore seqfile.txt alignment.hal 43 jobStore
44 seqfile.txt
45 alignment.full.hal
80 #end if 46 #end if
81 47
82 ]]></command> 48 ]]></command>
83 <inputs> 49 <inputs>
84 <conditional name="aln_mode"> 50 <conditional name="aln_mode">
109 </sanitizer> 75 </sanitizer>
110 <validator type="regex">[0-9a-zA-Z_]+</validator> 76 <validator type="regex">[0-9a-zA-Z_]+</validator>
111 </param> 77 </param>
112 <param name="fasta" type="data" format="fasta,fasta.gz" label="Genome Sequence" help="Input genome"/> 78 <param name="fasta" type="data" format="fasta,fasta.gz" label="Genome Sequence" help="Input genome"/>
113 </repeat> 79 </repeat>
114
115 <!-- add an option for root --> 80 <!-- add an option for root -->
116 <!-- root mr --> 81 <!-- root mr -->
117 </inputs> 82 </inputs>
118 <outputs> 83 <outputs>
119 <data name="out_hal" format="h5" from_work_dir="alignment.hal" label="${tool.name} on ${on_string} (HAL file)" /> 84 <data name="out_hal" format="h5" from_work_dir="alignment.full.hal" label="${tool.name} on ${on_string} (HAL file)">
85 </data>
120 <data name="out_gfa" format="gfa2.gz" from_work_dir="alignment.gfa.gz" label="${tool.name} on ${on_string} (GFA file)" > 86 <data name="out_gfa" format="gfa2.gz" from_work_dir="alignment.gfa.gz" label="${tool.name} on ${on_string} (GFA file)" >
121 <filter>aln_mode['aln_mode_select'] == 'intraspecies'</filter> 87 <filter>aln_mode['aln_mode_select'] == 'intraspecies'</filter>
122 </data> 88 </data>
123 </outputs> 89 </outputs>
124 <tests> 90 <tests>
180 <param name="label" value="simRat_chr6"/> 146 <param name="label" value="simRat_chr6"/>
181 <param name="fasta" value="simRat_chr6.fasta"/> 147 <param name="fasta" value="simRat_chr6.fasta"/>
182 </repeat> 148 </repeat>
183 <output name="out_hal"> 149 <output name="out_hal">
184 <assert_contents> 150 <assert_contents>
185 <has_size value="2088959" delta="200000" /> 151 <has_size value="565214" delta="65214" />
186 </assert_contents> 152 </assert_contents>
187 </output> 153 </output>
188 <output name="out_gfa"> 154 <output name="out_gfa">
189 <assert_contents> 155 <assert_contents>
190 <has_size value="173000" delta="200000" /> 156 <has_size value="173000" delta="200000" />