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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus commit 8fc43fe1e8c12438a14dbd174a8af3e7cb8b55dc
author iuc
date Thu, 08 Feb 2024 08:52:28 +0000
parents 9eeb13a92d79
children
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1 <tool id="cactus_cactus" name="Cactus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
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2 <description>whole-genome multiple sequence alignment</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="xrefs"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9
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10 ## Set up seqfile
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12 #if $aln_mode.aln_mode_select == 'interspecies':
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13 cat $aln_mode.in_tree >> seqfile.txt &&
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14 #end if
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15 #for $seq in $in_seqs:
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16 #set seq_fn = str($seq.label) + '.' + $seq.fasta.ext
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17 ln -s '$seq.fasta' '$seq_fn' &&
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18 printf '%s %s\n' '$seq.label' '$seq_fn' >> seqfile.txt
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19 &&
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20 #end for
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22 ## Run cactus
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24 #if $aln_mode.aln_mode_select == 'intraspecies':
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25 ## Run cactus-pangenome
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26 ## --reference should be the first argument
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27 ## https://github.com/ComparativeGenomicsToolkit/cactus/issues/1093#issuecomment-1620088688
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28 cactus-pangenome
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29 --reference $aln_mode.ref_level
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30 --binariesMode local
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31 --maxCores \${GALAXY_SLOTS:-4}
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32 --maxMemory \${GALAXY_MEMORY_MB:-16384}M
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33 --outDir ./
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34 --outName alignment
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35 jobStore
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36 seqfile.txt
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37 #else if $aln_mode.aln_mode_select == 'interspecies':
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38 ## Run cactus normally
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39 cactus
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40 --binariesMode local
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41 --maxCores \${GALAXY_SLOTS:-4}
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42 --maxMemory \${GALAXY_MEMORY_MB:-16384}M
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43 --workDir ./
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44 jobStore
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45 seqfile.txt
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46 alignment.full.hal
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47 #end if
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48
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49 ]]></command>
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50 <inputs>
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51 <conditional name="aln_mode">
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52 <param name="aln_mode_select" type="select" label="Alignment mode" help="The taxonomic relationship between input genomes. If genomes are from multiple individuals of the same species, select 'Within-species'">
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53 <option value="interspecies" selected="true">Between-species</option>
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54 <option value="intraspecies">Within-species</option>
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55 </param>
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56 <when value="interspecies">
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57 <param name="in_tree" type="data" format="nhx" label="Guide tree" help="Phylogenetic tree in Newick format. Required by Cactus to achieve linear scaling with number of input genomes"/>
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58 </when>
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59 <when value="intraspecies">
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60 <param name="ref_level" type="text" value="" label="Reference genome" help="Pangenomes from Minigraph-Cactus depend on a predetermined reference genome. Specify one of the Input Genomes as the reference genome. This must match the label used in 'Genome Label'.">
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61 <sanitizer invalid_char="">
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62 <valid initial="string.letters,string.digits">
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63 <add value="_"/>
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64 </valid>
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65 </sanitizer>
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66 <validator type="regex">[0-9a-zA-Z_]+</validator>
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67 </param>
0
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68 </when>
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69 </conditional>
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70 <repeat name="in_seqs" title="Input genome">
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71 <param name="label" type="text" value="" label="Genome label" help="NO SPACES. Must match a label in the guide tree.">
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72 <sanitizer invalid_char="">
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73 <valid initial="string.letters,string.digits">
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74 <add value="_"/>
6
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75 </valid>
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76 </sanitizer>
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77 <validator type="regex">[0-9a-zA-Z_]+</validator>
0
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78 </param>
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79 <param name="fasta" type="data" format="fasta,fasta.gz" label="Genome Sequence" help="Input genome"/>
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80 </repeat>
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81 <!-- add an option for root -->
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82 <!-- root mr -->
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83 </inputs>
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84 <outputs>
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85 <data name="out_hal" format="h5" from_work_dir="alignment.full.hal" label="${tool.name} on ${on_string} (HAL file)">
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86 </data>
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87 <data name="out_gfa" format="gfa2.gz" from_work_dir="alignment.gfa.gz" label="${tool.name} on ${on_string} (GFA file)">
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88 <filter>aln_mode['aln_mode_select'] == 'intraspecies'</filter>
4
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89 </data>
0
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90 </outputs>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
91 <tests>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
92 <!-- test interspecies mode -->
5
48c13389050d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ba63cf533f414ebc8f17bbe4b6ea852b561dd7d1
galaxy-australia
parents: 4
diff changeset
93 <test expect_num_outputs="1">
0
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
94 <conditional name="aln_mode">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
95 <param name="aln_mode_select" value="interspecies"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
96 <param name="in_tree" value="test_tree.nhx"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
97 </conditional>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
98 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
99 <param name="label" value="simCow_chr6"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
100 <param name="fasta" value="simCow_chr6.fasta"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
101 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
102 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
103 <param name="label" value="simDog_chr6"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
104 <param name="fasta" value="simDog_chr6.fasta"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
105 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
106 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
107 <param name="label" value="simHuman_chr6"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
108 <param name="fasta" value="simHuman_chr6.fasta"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
109 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
110 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
111 <param name="label" value="simMouse_chr6"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
112 <param name="fasta" value="simMouse_chr6.fasta"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
113 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
114 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
115 <param name="label" value="simRat_chr6"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
116 <param name="fasta" value="simRat_chr6.fasta"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
117 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
118 <output name="out_hal">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
119 <assert_contents>
15
098506c54016 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus commit 8fc43fe1e8c12438a14dbd174a8af3e7cb8b55dc
iuc
parents: 13
diff changeset
120 <has_size value="4472551" delta="200000"/>
0
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
121 </assert_contents>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
122 </output>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
123 </test>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
124 <!-- within-species mode -->
4
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
125 <test expect_num_outputs="2">
0
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
126 <conditional name="aln_mode">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
127 <param name="aln_mode_select" value="intraspecies"/>
4
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
128 <param name="ref_level" value="simCow_chr6"/>
0
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
129 </conditional>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
130 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
131 <param name="label" value="simCow_chr6"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
132 <param name="fasta" value="simCow_chr6.fasta"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
133 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
134 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
135 <param name="label" value="simDog_chr6"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
136 <param name="fasta" value="simDog_chr6.fasta"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
137 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
138 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
139 <param name="label" value="simHuman_chr6"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
140 <param name="fasta" value="simHuman_chr6.fasta"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
141 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
142 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
143 <param name="label" value="simMouse_chr6"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
144 <param name="fasta" value="simMouse_chr6.fasta"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
145 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
146 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
147 <param name="label" value="simRat_chr6"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
148 <param name="fasta" value="simRat_chr6.fasta"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
149 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
150 <output name="out_hal">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
151 <assert_contents>
15
098506c54016 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus commit 8fc43fe1e8c12438a14dbd174a8af3e7cb8b55dc
iuc
parents: 13
diff changeset
152 <has_size value="565214" delta="65214"/>
4
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
153 </assert_contents>
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
154 </output>
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
155 <output name="out_gfa">
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
156 <assert_contents>
15
098506c54016 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus commit 8fc43fe1e8c12438a14dbd174a8af3e7cb8b55dc
iuc
parents: 13
diff changeset
157 <has_size value="173000" delta="200000"/>
4
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
158 </assert_contents>
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
159 </output>
0
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
160 </test>
3
9422c5a87ee2 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit a2c67f11b7e96be2babfdf8a60cb2e2eb181ffe9"
galaxy-australia
parents: 2
diff changeset
161 <!-- FASTA header with spaces (used to fail) -->
4
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
162 <test expect_num_outputs="2">
0
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
163 <conditional name="aln_mode">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
164 <param name="aln_mode_select" value="intraspecies"/>
4
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
165 <param name="ref_level" value="badheader1"/>
0
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
166 </conditional>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
167 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
168 <param name="label" value="badheader1"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
169 <param name="fasta" value="bh1.fasta.gz"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
170 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
171 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
172 <param name="label" value="badheader2"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
173 <param name="fasta" value="bh2.fasta.gz"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
174 </repeat>
3
9422c5a87ee2 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit a2c67f11b7e96be2babfdf8a60cb2e2eb181ffe9"
galaxy-australia
parents: 2
diff changeset
175 <output name="out_hal">
9422c5a87ee2 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit a2c67f11b7e96be2babfdf8a60cb2e2eb181ffe9"
galaxy-australia
parents: 2
diff changeset
176 <assert_contents>
15
098506c54016 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus commit 8fc43fe1e8c12438a14dbd174a8af3e7cb8b55dc
iuc
parents: 13
diff changeset
177 <has_size value="3382274" delta="200000"/>
3
9422c5a87ee2 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit a2c67f11b7e96be2babfdf8a60cb2e2eb181ffe9"
galaxy-australia
parents: 2
diff changeset
178 </assert_contents>
9422c5a87ee2 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit a2c67f11b7e96be2babfdf8a60cb2e2eb181ffe9"
galaxy-australia
parents: 2
diff changeset
179 </output>
4
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
180 <output name="out_gfa">
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
181 <assert_contents>
15
098506c54016 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus commit 8fc43fe1e8c12438a14dbd174a8af3e7cb8b55dc
iuc
parents: 13
diff changeset
182 <has_size value="764748" delta="200000"/>
4
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
183 </assert_contents>
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
184 </output>
0
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
185 </test>
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186 </tests>
15
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187 <help><![CDATA[
6
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188
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189 .. class:: infomark
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190
0
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191 **What it does**
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192
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193 `Cactus <https://github.com/ComparativeGenomicsToolkit/cactus>`__ is a
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194 reference-free whole-genome multiple alignment program. It can be used
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195 to progressively align a large number of genomes.
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196
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197 -----
a74dbfee5a86 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
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198
a74dbfee5a86 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
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199 .. class:: infomark
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200
0
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201 **Usage**
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202
4
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203 **Between-species mode (Progressive Cactus)**
0
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204
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205 If you are aligning genomes from **multiple species**, you need to
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206 provide a guide tree in Newick format. Cactus uses the guide tree to
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207 progressively align genomes, meaning that it doesn’t need to align all
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208 possible pairs of genomes.
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209
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210 A Newick-formatted tree for human, chimp and gorilla genomes looks like
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211 this:
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212
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213 ::
0
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214
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215 (((human:0.006,chimp:0.006667):0.0022,gorilla:0.008825):0.0096,orang:0.01831);
0
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216
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217 The numbers are the branch lengths.
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218
4
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219 **Within-species mode (Minigraph-Cactus)**
0
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220
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221 You can also run Cactus in `pangenome
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222 mode <https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md>`__
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223 to align genomes of multiple individuals from the **same species**. In
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224 this mode you will not use a guide tree. Cactus will use
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225 `minigraph <https://github.com/lh3/minigraph>`__ to generate a graph of
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226 the input genomes and then use the graph to order the alignments. To use
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227 pangenome mode, select ‘Within-species’ in the ‘Alignment mode’
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228 dropdown.
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229
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230 Unlike Between-species mode, Within-species mode depends on a predetermined reference genome.
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231
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232 -----
a74dbfee5a86 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
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233
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234 .. class:: infomark
4
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235
0
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236 **Input**
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237
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238 The developers recommend soft-masking your genomes with RepeatMasker
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239 before running Cactus. RepeatMasker is available on Galaxy.
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240
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241 If you’re using Between-species mode, you need to provide labels for the
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242 fasta files that match the leaves on the guide tree. In the example
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243 above, you would use the label ‘human’ for the human fasta file.
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244
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245 -----
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246
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247 .. class:: infomark
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248
0
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249 **Output**
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250
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251 The main output of Cactus is in `HAL
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252 format <https://github.com/ComparativeGenomicsToolkit/cactus#using-the-output>`__.
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253 You can use the `Cactus: export <root?tool_id=cactus_export>`__ tool to
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254 convert the Cactus output to a VG or Multiple Alignment Format (MAF)
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255 file.
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256
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257
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258 ]]></help>
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259 <expand macro="citations"/>
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260 </tool>