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annotate 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
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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 export TMPDIR=\${_GALAXY_JOB_TMP_DIR} &&
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10
0
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11 ## Set up seqfile
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13 #if $aln_mode.aln_mode_select == 'interspecies':
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14 cat $aln_mode.in_tree >> seqfile.txt &&
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15 #end if
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16 #for $seq in $in_seqs:
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17 #set seq_fn = str($seq.label) + '.' + $seq.fasta.ext
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18 ln -s '$seq.fasta' '$seq_fn' &&
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19 printf '%s %s\n' '$seq.label' '$seq_fn' >> seqfile.txt
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20 &&
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21 #end for
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23 ## Run cactus
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25 #if $aln_mode.aln_mode_select == 'intraspecies':
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26 ## Run cactus-pangenome
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27 ## --reference should be the first argument
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28 ## https://github.com/ComparativeGenomicsToolkit/cactus/issues/1093#issuecomment-1620088688
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29 cactus-pangenome
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30 --reference $aln_mode.ref_level
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31 --binariesMode local
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32 --maxCores \${GALAXY_SLOTS:-4}
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33 --maxMemory \${GALAXY_MEMORY_MB:-8192}M
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34 --outDir ./
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35 --outName alignment
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36 jobStore
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37 seqfile.txt
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38 #else if $aln_mode.aln_mode_select == 'interspecies':
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39 ## Run cactus normally
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40 cactus
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41 --binariesMode local
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42 --maxCores \${GALAXY_SLOTS:-4}
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43 --maxMemory \${GALAXY_MEMORY_MB:-8192}M
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44 --workDir ./
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45 jobStore
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46 seqfile.txt
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47 alignment.full.hal
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48 #end if
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49
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50 ]]></command>
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51 <inputs>
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52 <conditional name="aln_mode">
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53 <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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54 <option value="interspecies" selected="true">Between-species</option>
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55 <option value="intraspecies">Within-species</option>
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56 </param>
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57 <when value="interspecies">
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58 <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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59 </when>
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60 <when value="intraspecies">
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61 <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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62 <sanitizer invalid_char="">
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63 <valid initial="string.letters,string.digits">
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64 <add value="_" />
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65 </valid>
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66 </sanitizer>
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67 <validator type="regex">[0-9a-zA-Z_]+</validator>
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68 </param>
0
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69 </when>
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70 </conditional>
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71 <repeat name="in_seqs" title="Input genome">
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72 <param name="label" type="text" value="" label="Genome label" help="NO SPACES. Must match a label in the guide tree.">
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73 <sanitizer invalid_char="">
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74 <valid initial="string.letters,string.digits">
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75 <add value="_" />
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76 </valid>
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77 </sanitizer>
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78 <validator type="regex">[0-9a-zA-Z_]+</validator>
0
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79 </param>
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80 <param name="fasta" type="data" format="fasta,fasta.gz" label="Genome Sequence" help="Input genome"/>
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81 </repeat>
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82 <!-- add an option for root -->
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83 <!-- root mr -->
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84 </inputs>
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85 <outputs>
12
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86 <data name="out_hal" format="h5" from_work_dir="alignment.full.hal" label="${tool.name} on ${on_string} (HAL file)">
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87 </data>
4
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88 <data name="out_gfa" format="gfa2.gz" from_work_dir="alignment.gfa.gz" label="${tool.name} on ${on_string} (GFA file)" >
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89 <filter>aln_mode['aln_mode_select'] == 'intraspecies'</filter>
4
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90 </data>
0
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parents:
diff changeset
91 </outputs>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
92 <tests>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
93 <!-- test interspecies mode -->
5
48c13389050d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ba63cf533f414ebc8f17bbe4b6ea852b561dd7d1
galaxy-australia
parents: 4
diff changeset
94 <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
95 <conditional name="aln_mode">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
96 <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
97 <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
98 </conditional>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
99 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
100 <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
101 <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
102 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
103 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
104 <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
105 <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
106 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
107 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
108 <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
109 <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
110 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
111 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
112 <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
113 <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
114 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
115 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
116 <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
117 <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
118 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
119 <output name="out_hal">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
120 <assert_contents>
6
a74dbfee5a86 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
galaxy-australia
parents: 5
diff changeset
121 <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
122 </assert_contents>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
123 </output>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
124 </test>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
125 <!-- within-species mode -->
4
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
126 <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
127 <conditional name="aln_mode">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
128 <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
129 <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
130 </conditional>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
131 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
132 <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
133 <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
134 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
135 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
136 <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
137 <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
138 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
139 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
140 <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
141 <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
142 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
143 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
144 <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
145 <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
146 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
147 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
148 <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
149 <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
150 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
151 <output name="out_hal">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
152 <assert_contents>
12
2263989660f5 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cb75f42cdcae1a92023e6e5b33a8a260877d76fe
galaxy-australia
parents: 7
diff changeset
153 <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
154 </assert_contents>
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
155 </output>
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
156 <output name="out_gfa">
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
157 <assert_contents>
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
158 <has_size value="173000" delta="200000" />
0
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
159 </assert_contents>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
160 </output>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
161 </test>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
162 <!-- compressed input -->
4
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
163 <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
164 <conditional name="aln_mode">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
165 <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
166 <param name="ref_level" value="germ_25"/>
0
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
167 </conditional>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
168 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
169 <param name="label" value="germ_25"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
170 <param name="fasta" value="germ_25.fasta.gz"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
171 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
172 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
173 <param name="label" value="vulg_25"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
174 <param name="fasta" value="vulg_25.fasta.gz"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
175 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
176 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
177 <param name="label" value="pens_25"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
178 <param name="fasta" value="pens_25.fasta.gz"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
179 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
180 <output name="out_hal">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
181 <assert_contents>
13
9eeb13a92d79 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2d431863824af49c82ff2ae318abee3b16141a4e
galaxy-australia
parents: 12
diff changeset
182 <has_size value="6235006" delta="200000" />
0
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
183 </assert_contents>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
184 </output>
4
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
185 <output name="out_gfa">
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
186 <assert_contents>
13
9eeb13a92d79 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2d431863824af49c82ff2ae318abee3b16141a4e
galaxy-australia
parents: 12
diff changeset
187 <has_size value="5771414" delta="200000" />
4
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
188 </assert_contents>
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
189 </output>
0
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
190 </test>
3
9422c5a87ee2 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit a2c67f11b7e96be2babfdf8a60cb2e2eb181ffe9"
galaxy-australia
parents: 2
diff changeset
191 <!-- 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
192 <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
193 <conditional name="aln_mode">
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galaxy-australia
parents:
diff changeset
194 <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
195 <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
196 </conditional>
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galaxy-australia
parents:
diff changeset
197 <repeat name="in_seqs">
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galaxy-australia
parents:
diff changeset
198 <param name="label" value="badheader1"/>
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galaxy-australia
parents:
diff changeset
199 <param name="fasta" value="bh1.fasta.gz"/>
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galaxy-australia
parents:
diff changeset
200 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
201 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
202 <param name="label" value="badheader2"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
203 <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
204 </repeat>
3
9422c5a87ee2 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit a2c67f11b7e96be2babfdf8a60cb2e2eb181ffe9"
galaxy-australia
parents: 2
diff changeset
205 <output name="out_hal">
9422c5a87ee2 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit a2c67f11b7e96be2babfdf8a60cb2e2eb181ffe9"
galaxy-australia
parents: 2
diff changeset
206 <assert_contents>
9422c5a87ee2 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit a2c67f11b7e96be2babfdf8a60cb2e2eb181ffe9"
galaxy-australia
parents: 2
diff changeset
207 <has_size value="3382274" delta="200000" />
9422c5a87ee2 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit a2c67f11b7e96be2babfdf8a60cb2e2eb181ffe9"
galaxy-australia
parents: 2
diff changeset
208 </assert_contents>
9422c5a87ee2 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit a2c67f11b7e96be2babfdf8a60cb2e2eb181ffe9"
galaxy-australia
parents: 2
diff changeset
209 </output>
4
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
210 <output name="out_gfa">
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
211 <assert_contents>
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
212 <has_size value="764748" delta="200000" />
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
213 </assert_contents>
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
214 </output>
0
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galaxy-australia
parents:
diff changeset
215 </test>
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galaxy-australia
parents:
diff changeset
216 </tests>
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galaxy-australia
parents:
diff changeset
217 <help><![CDATA[
6
a74dbfee5a86 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
galaxy-australia
parents: 5
diff changeset
218
a74dbfee5a86 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
galaxy-australia
parents: 5
diff changeset
219 .. class:: infomark
a74dbfee5a86 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
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220
0
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parents:
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221 **What it does**
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galaxy-australia
parents:
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222
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galaxy-australia
parents:
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223 `Cactus <https://github.com/ComparativeGenomicsToolkit/cactus>`__ is a
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
224 reference-free whole-genome multiple alignment program. It can be used
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
225 to progressively align a large number of genomes.
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galaxy-australia
parents:
diff changeset
226
6
a74dbfee5a86 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
galaxy-australia
parents: 5
diff changeset
227 -----
a74dbfee5a86 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
galaxy-australia
parents: 5
diff changeset
228
a74dbfee5a86 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
galaxy-australia
parents: 5
diff changeset
229 .. class:: infomark
a74dbfee5a86 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
galaxy-australia
parents: 5
diff changeset
230
0
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galaxy-australia
parents:
diff changeset
231 **Usage**
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galaxy-australia
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232
4
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
233 **Between-species mode (Progressive Cactus)**
0
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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parents:
diff changeset
234
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galaxy-australia
parents:
diff changeset
235 If you are aligning genomes from **multiple species**, you need to
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
236 provide a guide tree in Newick format. Cactus uses the guide tree to
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
237 progressively align genomes, meaning that it doesn’t need to align all
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
238 possible pairs of genomes.
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
239
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
240 A Newick-formatted tree for human, chimp and gorilla genomes looks like
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
241 this:
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
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242
6
a74dbfee5a86 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
galaxy-australia
parents: 5
diff changeset
243 ::
0
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
244
6
a74dbfee5a86 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
galaxy-australia
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diff changeset
245 (((human:0.006,chimp:0.006667):0.0022,gorilla:0.008825):0.0096,orang:0.01831);
0
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galaxy-australia
parents:
diff changeset
246
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
247 The numbers are the branch lengths.
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parents:
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248
4
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
249 **Within-species mode (Minigraph-Cactus)**
0
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galaxy-australia
parents:
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250
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galaxy-australia
parents:
diff changeset
251 You can also run Cactus in `pangenome
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galaxy-australia
parents:
diff changeset
252 mode <https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md>`__
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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parents:
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253 to align genomes of multiple individuals from the **same species**. In
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
254 this mode you will not use a guide tree. Cactus will use
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
255 `minigraph <https://github.com/lh3/minigraph>`__ to generate a graph of
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
256 the input genomes and then use the graph to order the alignments. To use
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
257 pangenome mode, select ‘Within-species’ in the ‘Alignment mode’
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galaxy-australia
parents:
diff changeset
258 dropdown.
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galaxy-australia
parents:
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259
6
a74dbfee5a86 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
galaxy-australia
parents: 5
diff changeset
260 Unlike Between-species mode, Within-species mode depends on a predetermined reference genome.
a74dbfee5a86 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
galaxy-australia
parents: 5
diff changeset
261
a74dbfee5a86 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
galaxy-australia
parents: 5
diff changeset
262 -----
a74dbfee5a86 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
galaxy-australia
parents: 5
diff changeset
263
a74dbfee5a86 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
galaxy-australia
parents: 5
diff changeset
264 .. class:: infomark
4
3c8227556fdc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2b4c7c63b0e4a1f730794a4a5825bce29ee2eb25
galaxy-australia
parents: 3
diff changeset
265
0
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galaxy-australia
parents:
diff changeset
266 **Input**
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galaxy-australia
parents:
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267
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galaxy-australia
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268 The developers recommend soft-masking your genomes with RepeatMasker
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galaxy-australia
parents:
diff changeset
269 before running Cactus. RepeatMasker is available on Galaxy.
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270
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galaxy-australia
parents:
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271 If you’re using Between-species mode, you need to provide labels for the
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galaxy-australia
parents:
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272 fasta files that match the leaves on the guide tree. In the example
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galaxy-australia
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273 above, you would use the label ‘human’ for the human fasta file.
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274
6
a74dbfee5a86 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
galaxy-australia
parents: 5
diff changeset
275 -----
a74dbfee5a86 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
galaxy-australia
parents: 5
diff changeset
276
a74dbfee5a86 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
galaxy-australia
parents: 5
diff changeset
277 .. class:: infomark
a74dbfee5a86 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
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278
0
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galaxy-australia
parents:
diff changeset
279 **Output**
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galaxy-australia
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280
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galaxy-australia
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diff changeset
281 The main output of Cactus is in `HAL
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galaxy-australia
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282 format <https://github.com/ComparativeGenomicsToolkit/cactus#using-the-output>`__.
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galaxy-australia
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283 You can use the `Cactus: export <root?tool_id=cactus_export>`__ tool to
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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284 convert the Cactus output to a VG or Multiple Alignment Format (MAF)
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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285 file.
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286
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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287
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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288 ]]></help>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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289 <expand macro="citations"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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290 </tool>