Mercurial > repos > galaxy-australia > cactus_cactus

annotate cactus_cactus.xml @ 3:9422c5a87ee2 draft

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"planemo upload for repository https://github.com/usegalaxy-au/tools-au commit a2c67f11b7e96be2babfdf8a60cb2e2eb181ffe9"
author galaxy-australia
date Tue, 20 Sep 2022 05:38:05 +0000
parents 8b67dd48fec1
children 3c8227556fdc
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85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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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>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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6 <expand macro="xrefs"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ## Set up seqfile
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10
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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11 #if $aln_mode.aln_mode_select == 'interspecies':
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12 cat $aln_mode.in_tree >> seqfile.txt &&
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13 #end if
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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14 #set seq_line = ''
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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 #set seq_line += $seq_fn + ' '
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20 &&
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21 #end for
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22
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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23 ## Run cactus
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24
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25 #if $aln_mode.aln_mode_select == 'intraspecies':
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26 ## If we're doing a pangenome, we need to run the steps manually
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27 minigraph -xggs
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28 -t \${GALAXY_SLOTS:-4}
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29 $seq_line
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30 > pangenome.gfa
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31 &&
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32 cactus-graphmap
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33 --maxCores \${GALAXY_SLOTS:-4}
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34 --maxMemory \${GALAXY_MEMORY_MB:-8192}M
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35 ./jobStore
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36 ./seqfile.txt
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37 pangenome.gfa
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38 pangenome.paf
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39 --outputFasta pangenome.gfa.fa
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40 --binariesMode local
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41 --workDir ./
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42 &&
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43 cactus-align
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44 --maxCores \${GALAXY_SLOTS:-4}
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45 --maxMemory \${GALAXY_MEMORY_MB:-8192}M
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46 ./jobStore
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47 ./seqfile.txt
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48 pangenome.paf
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49 alignment.hal
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50 --pangenome
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51 --binariesMode local
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52 --workDir ./
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53 #else if $aln_mode.aln_mode_select == 'interspecies':
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54 ## Run cactus normally
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55 cactus
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56 --maxCores \${GALAXY_SLOTS:-4}
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57 --maxMemory \${GALAXY_MEMORY_MB:-8192}M
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58 jobStore seqfile.txt alignment.hal
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59 --binariesMode local
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60 --workDir ./
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61 #end if
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62
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63 ]]></command>
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64 <inputs>
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65 <conditional name="aln_mode">
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66 <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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67 <option value="interspecies" selected="true">Between-species</option>
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68 <option value="intraspecies">Within-species</option>
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69 </param>
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70 <when value="interspecies">
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71 <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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72 </when>
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73 <when value="intraspecies">
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74 </when>
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75 </conditional>
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76 <repeat name="in_seqs" title="Input genome">
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77 <param name="label" type="text" value="" label="Genome Label" help="NO SPACES. Must match a label in the guide tree.">
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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.hal" label="${tool.name} on ${on_string} (HAL file)" />
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86 </outputs>
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87 <tests>
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88 <!-- test interspecies mode -->
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89 <test expect_num_outputs="1">
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90 <conditional name="aln_mode">
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91 <param name="aln_mode_select" value="interspecies"/>
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92 <param name="in_tree" value="test_tree.nhx"/>
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93 </conditional>
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94 <repeat name="in_seqs">
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parents:
diff changeset
95 <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
96 <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
97 </repeat>
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="simDog_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="simDog_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="simHuman_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="simHuman_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="simMouse_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="simMouse_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="simRat_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="simRat_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 <output name="out_hal">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
115 <assert_contents>
2
8b67dd48fec1 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit b2235e7e7970f74e5d55ce150e3380d93fcdd70f
galaxy-australia
parents: 1
diff changeset
116 <has_size value="4783905" delta="200000" />
0
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
117 </assert_contents>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
118 </output>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
119 </test>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
120 <!-- within-species mode -->
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
121 <test expect_num_outputs="1">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
122 <conditional name="aln_mode">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
123 <param name="aln_mode_select" value="intraspecies"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
124 </conditional>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
125 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
126 <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
127 <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
128 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
129 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
130 <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
131 <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
132 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
133 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
134 <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
135 <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
136 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
137 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
138 <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
139 <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
140 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
141 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
142 <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
143 <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
144 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
145 <output name="out_hal">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
146 <assert_contents>
2
8b67dd48fec1 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit b2235e7e7970f74e5d55ce150e3380d93fcdd70f
galaxy-australia
parents: 1
diff changeset
147 <has_size value="1349620" delta="200000" />
0
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
148 </assert_contents>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
149 </output>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
150 </test>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
151 <!-- compressed input -->
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
152 <test expect_num_outputs="1">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
153 <conditional name="aln_mode">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
154 <param name="aln_mode_select" value="intraspecies"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
155 </conditional>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
156 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
157 <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
158 <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
159 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
160 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
161 <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
162 <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
163 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
164 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
165 <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
166 <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
167 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
168 <output name="out_hal">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
169 <assert_contents>
2
8b67dd48fec1 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit b2235e7e7970f74e5d55ce150e3380d93fcdd70f
galaxy-australia
parents: 1
diff changeset
170 <has_size value="7420424" delta="200000" />
0
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
171 </assert_contents>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
172 </output>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
173 </test>
3
9422c5a87ee2 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit a2c67f11b7e96be2babfdf8a60cb2e2eb181ffe9"
galaxy-australia
parents: 2
diff changeset
174 <!-- FASTA header with spaces (used to fail) -->
9422c5a87ee2 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit a2c67f11b7e96be2babfdf8a60cb2e2eb181ffe9"
galaxy-australia
parents: 2
diff changeset
175 <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
176 <conditional name="aln_mode">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
177 <param name="aln_mode_select" value="intraspecies"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
178 </conditional>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
179 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
180 <param name="label" value="badheader1"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
181 <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
182 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
183 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
184 <param name="label" value="badheader2"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
185 <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
186 </repeat>
3
9422c5a87ee2 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit a2c67f11b7e96be2babfdf8a60cb2e2eb181ffe9"
galaxy-australia
parents: 2
diff changeset
187 <output name="out_hal">
9422c5a87ee2 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit a2c67f11b7e96be2babfdf8a60cb2e2eb181ffe9"
galaxy-australia
parents: 2
diff changeset
188 <assert_contents>
9422c5a87ee2 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit a2c67f11b7e96be2babfdf8a60cb2e2eb181ffe9"
galaxy-australia
parents: 2
diff changeset
189 <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
190 </assert_contents>
9422c5a87ee2 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit a2c67f11b7e96be2babfdf8a60cb2e2eb181ffe9"
galaxy-australia
parents: 2
diff changeset
191 </output>
0
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192 </test>
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193 </tests>
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194 <help><![CDATA[
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195 **What it does**
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196
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197 `Cactus <https://github.com/ComparativeGenomicsToolkit/cactus>`__ is a
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198 reference-free whole-genome multiple alignment program. It can be used
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199 to progressively align a large number of genomes.
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200
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201 **Usage**
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202
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203 **Between-species mode**
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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 ::
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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);
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216
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217 The numbers are the branch lengths.
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218
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219 **Beta: Within-species mode**
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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 **Input**
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231
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232 The developers recommend soft-masking your genomes with RepeatMasker
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233 before running Cactus. RepeatMasker is available on Galaxy.
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234
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235 If you’re using Between-species mode, you need to provide labels for the
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236 fasta files that match the leaves on the guide tree. In the example
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237 above, you would use the label ‘human’ for the human fasta file.
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238
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239 **Output**
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240
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241 The main output of Cactus is in `HAL
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242 format <https://github.com/ComparativeGenomicsToolkit/cactus#using-the-output>`__.
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243 You can use the `Cactus: export <root?tool_id=cactus_export>`__ tool to
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244 convert the Cactus output to a VG or Multiple Alignment Format (MAF)
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245 file.
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246
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247
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248 ]]></help>
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249 <expand macro="citations"/>
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250 </tool>