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annotate cactus_cactus.xml @ 2:8b67dd48fec1 draft

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planemo upload for repository https://github.com/usegalaxy-au/tools-au commit b2235e7e7970f74e5d55ce150e3380d93fcdd70f
author galaxy-australia
date Tue, 13 Sep 2022 00:17:17 +0000
parents 1bc1199f0ff4
children 9422c5a87ee2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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>
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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 ## Check the FASTA headers
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10 ## This is only necessary in pangenome mode
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11 #if $aln_mode.aln_mode_select == 'intraspecies':
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12 #for $seq in $in_seqs:
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13 if
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14 #if $seq.fasta.is_of_type('fasta.gz'):
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15 zgrep
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16 #else
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17 grep
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18 #end if
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19 "^>" $seq.fasta | grep -q "[[:space:]]" ; then
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20 echo "Error parsing input FASTA." ;
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21 echo "Pangenome mode fails if there are spaces in the header." ;
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22 echo "Please remove them with the NormalizeFasta tool." ;
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23 exit 1
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24 ; fi &&
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25 #end for
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26 #end if
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27
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28 ## Set up seqfile
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29
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30 #if $aln_mode.aln_mode_select == 'interspecies':
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31 cat $aln_mode.in_tree >> seqfile.txt &&
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32 #end if
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33 #set seq_line = ''
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34 #for $seq in $in_seqs:
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35 #set seq_fn = str($seq.label) + '.' + $seq.fasta.ext
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36 ln -s '$seq.fasta' '$seq_fn' &&
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37 printf '%s %s\n' '$seq.label' '$seq_fn' >> seqfile.txt
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38 #set seq_line += $seq_fn + ' '
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39 &&
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40 #end for
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41
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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42 ## Run cactus
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43
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44 #if $aln_mode.aln_mode_select == 'intraspecies':
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45 ## If we're doing a pangenome, we need to run the steps manually
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46 minigraph -xggs
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47 -t \${GALAXY_SLOTS:-4}
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48 $seq_line
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49 > pangenome.gfa
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50 &&
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51 cactus-graphmap
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52 --maxCores \${GALAXY_SLOTS:-4}
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53 --maxMemory \${GALAXY_MEMORY_MB:-8192}M
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54 ./jobStore
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55 ./seqfile.txt
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56 pangenome.gfa
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57 pangenome.paf
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58 --outputFasta pangenome.gfa.fa
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59 --binariesMode local
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60 --workDir ./
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61 &&
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62 cactus-align
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63 --maxCores \${GALAXY_SLOTS:-4}
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64 --maxMemory \${GALAXY_MEMORY_MB:-8192}M
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65 ./jobStore
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66 ./seqfile.txt
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67 pangenome.paf
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68 alignment.hal
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69 --pangenome
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70 --binariesMode local
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71 --workDir ./
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72 #else if $aln_mode.aln_mode_select == 'interspecies':
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73 ## Run cactus normally
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74 cactus
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75 --maxCores \${GALAXY_SLOTS:-4}
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76 --maxMemory \${GALAXY_MEMORY_MB:-8192}M
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77 jobStore seqfile.txt alignment.hal
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78 --binariesMode local
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79 --workDir ./
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80 #end if
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81
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82 ]]></command>
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83 <inputs>
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84 <conditional name="aln_mode">
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85 <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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86 <option value="interspecies" selected="true">Between-species</option>
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87 <option value="intraspecies">Within-species</option>
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88 </param>
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89 <when value="interspecies">
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90 <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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91 </when>
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92 <when value="intraspecies">
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93 </when>
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94 </conditional>
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95 <repeat name="in_seqs" title="Input genome">
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galaxy-australia
parents:
diff changeset
96 <param name="label" type="text" value="" label="Genome Label" help="NO SPACES. Must match a label in the guide tree.">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
97 </param>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
98 <param name="fasta" type="data" format="fasta,fasta.gz" label="Genome Sequence" help="Input genome"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
99 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
100 <!-- add an option for root -->
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
101 <!-- root mr -->
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
102 </inputs>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
103 <outputs>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
104 <data name="out_hal" format="h5" from_work_dir="alignment.hal" label="${tool.name} on ${on_string} (HAL file)" />
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
105 </outputs>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
106 <tests>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
107 <!-- test interspecies mode -->
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
108 <test expect_num_outputs="1">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
109 <conditional name="aln_mode">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
110 <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
111 <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
112 </conditional>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
113 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
114 <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
115 <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
116 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
117 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
118 <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
119 <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
120 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
121 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
122 <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
123 <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
124 </repeat>
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="simMouse_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="simMouse_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="simRat_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="simRat_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 <output name="out_hal">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
134 <assert_contents>
2
8b67dd48fec1 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit b2235e7e7970f74e5d55ce150e3380d93fcdd70f
galaxy-australia
parents: 1
diff changeset
135 <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
136 </assert_contents>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
137 </output>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
138 </test>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
139 <!-- within-species mode -->
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
140 <test expect_num_outputs="1">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
141 <conditional name="aln_mode">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
142 <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
143 </conditional>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
144 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
145 <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
146 <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
147 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
148 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
149 <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
150 <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
151 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
152 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
153 <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
154 <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
155 </repeat>
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="simMouse_chr6"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
158 <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
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="simRat_chr6"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
162 <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
163 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
164 <output name="out_hal">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
165 <assert_contents>
2
8b67dd48fec1 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit b2235e7e7970f74e5d55ce150e3380d93fcdd70f
galaxy-australia
parents: 1
diff changeset
166 <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
167 </assert_contents>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
168 </output>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
169 </test>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
170 <!-- compressed input -->
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
171 <test expect_num_outputs="1">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
172 <conditional name="aln_mode">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
173 <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
174 </conditional>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
175 <repeat name="in_seqs">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
176 <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
177 <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
178 </repeat>
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="vulg_25"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
181 <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
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="pens_25"/>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
185 <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
186 </repeat>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
187 <output name="out_hal">
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
188 <assert_contents>
2
8b67dd48fec1 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit b2235e7e7970f74e5d55ce150e3380d93fcdd70f
galaxy-australia
parents: 1
diff changeset
189 <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
190 </assert_contents>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
191 </output>
85f68b344286 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
diff changeset
192 </test>
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193 <!-- FASTA header -->
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194 <test expect_exit_code="1" expect_failure="true">
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195 <conditional name="aln_mode">
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196 <param name="aln_mode_select" value="intraspecies"/>
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197 </conditional>
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198 <repeat name="in_seqs">
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199 <param name="label" value="badheader1"/>
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200 <param name="fasta" value="bh1.fasta.gz"/>
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201 </repeat>
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202 <repeat name="in_seqs">
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203 <param name="label" value="badheader2"/>
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204 <param name="fasta" value="bh2.fasta.gz"/>
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205 </repeat>
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206 </test>
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207 </tests>
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208 <help><![CDATA[
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209 **What it does**
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210
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211 `Cactus <https://github.com/ComparativeGenomicsToolkit/cactus>`__ is a
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212 reference-free whole-genome multiple alignment program. It can be used
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213 to progressively align a large number of genomes.
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214
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215 **Usage**
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216
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217 **Between-species mode**
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218
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219 If you are aligning genomes from **multiple species**, you need to
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220 provide a guide tree in Newick format. Cactus uses the guide tree to
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221 progressively align genomes, meaning that it doesn’t need to align all
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222 possible pairs of genomes.
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223
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224 A Newick-formatted tree for human, chimp and gorilla genomes looks like
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225 this:
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226
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227 ::
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228
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229 (((human:0.006,chimp:0.006667):0.0022,gorilla:0.008825):0.0096,orang:0.01831);
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230
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231 The numbers are the branch lengths.
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232
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233 **Beta: Within-species mode**
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234
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235 You can also run Cactus in `pangenome
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236 mode <https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md>`__
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237 to align genomes of multiple individuals from the **same species**. In
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238 this mode you will not use a guide tree. Cactus will use
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239 `minigraph <https://github.com/lh3/minigraph>`__ to generate a graph of
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240 the input genomes and then use the graph to order the alignments. To use
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241 pangenome mode, select ‘Within-species’ in the ‘Alignment mode’
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242 dropdown.
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243
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244 ⚠️ To use pangenome mode, you will have to remove spaces from the headers in your FASTA file.
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245 You can do this with the NormalizeFasta tool.
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246
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247 **Input**
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248
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249 The developers recommend soft-masking your genomes with RepeatMasker
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250 before running Cactus. RepeatMasker is available on Galaxy.
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251
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252 If you’re using Between-species mode, you need to provide labels for the
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253 fasta files that match the leaves on the guide tree. In the example
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254 above, you would use the label ‘human’ for the human fasta file.
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255
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256 **Output**
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257
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258 The main output of Cactus is in `HAL
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259 format <https://github.com/ComparativeGenomicsToolkit/cactus#using-the-output>`__.
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260 You can use the `Cactus: export <root?tool_id=cactus_export>`__ tool to
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261 convert the Cactus output to a VG or Multiple Alignment Format (MAF)
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262 file.
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263
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264
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265 ]]></help>
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266 <expand macro="citations"/>
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267 </tool>