Mercurial > repos > iuc > cactus_cactus

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus commit 827619d22d2931d8fb34ed6844cfa91433e1ac2c
author iuc
date Tue, 06 Feb 2024 00:30:39 +0000
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51c3c42bc644 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus commit 827619d22d2931d8fb34ed6844cfa91433e1ac2c
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1 <tool id="cactus_cactus" name="Cactus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
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2 <description>whole-genome multiple sequence alignment</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="xrefs"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9
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10 ## Set up seqfile
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11
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12 #if $aln_mode.aln_mode_select == 'interspecies':
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13 cat $aln_mode.in_tree >> seqfile.txt &&
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14 #end if
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15 #for $seq in $in_seqs:
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16 #set seq_fn = str($seq.label) + '.' + $seq.fasta.ext
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17 ln -s '$seq.fasta' '$seq_fn' &&
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18 printf '%s %s\n' '$seq.label' '$seq_fn' >> seqfile.txt
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19 &&
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20 #end for
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21
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22 ## Run cactus
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23
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24 #if $aln_mode.aln_mode_select == 'intraspecies':
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25 ## Run cactus-pangenome
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26 ## --reference should be the first argument
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27 ## https://github.com/ComparativeGenomicsToolkit/cactus/issues/1093#issuecomment-1620088688
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28 cactus-pangenome
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29 --reference $aln_mode.ref_level
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30 --binariesMode local
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31 --maxCores \${GALAXY_SLOTS:-4}
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32 --maxMemory \${GALAXY_MEMORY_MB:-16384}M
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33 --outDir ./
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34 --outName alignment
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35 jobStore
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36 seqfile.txt
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37 #else if $aln_mode.aln_mode_select == 'interspecies':
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38 ## Run cactus normally
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39 cactus
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40 --binariesMode local
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41 --maxCores \${GALAXY_SLOTS:-4}
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42 --maxMemory \${GALAXY_MEMORY_MB:-16384}M
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43 --workDir ./
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44 jobStore
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45 seqfile.txt
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46 alignment.full.hal
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47 #end if
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48
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49 ]]></command>
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50 <inputs>
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51 <conditional name="aln_mode">
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52 <param name="aln_mode_select" type="select" label="Alignment mode" help="The taxonomic relationship between input genomes. If genomes are from multiple individuals of the same species, select 'Within-species'">
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53 <option value="interspecies" selected="true">Between-species</option>
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54 <option value="intraspecies">Within-species</option>
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55 </param>
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56 <when value="interspecies">
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57 <param name="in_tree" type="data" format="nhx" label="Guide tree" help="Phylogenetic tree in Newick format. Required by Cactus to achieve linear scaling with number of input genomes"/>
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58 </when>
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59 <when value="intraspecies">
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60 <param name="ref_level" type="text" value="" label="Reference genome" help="Pangenomes from Minigraph-Cactus depend on a predetermined reference genome. Specify one of the Input Genomes as the reference genome. This must match the label used in 'Genome Label'.">
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61 <sanitizer invalid_char="">
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62 <valid initial="string.letters,string.digits">
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63 <add value="_"/>
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64 </valid>
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65 </sanitizer>
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66 <validator type="regex">[0-9a-zA-Z_]+</validator>
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67 </param>
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68 </when>
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69 </conditional>
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70 <repeat name="in_seqs" title="Input genome">
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71 <param name="label" type="text" value="" label="Genome label" help="NO SPACES. Must match a label in the guide tree.">
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72 <sanitizer invalid_char="">
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73 <valid initial="string.letters,string.digits">
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74 <add value="_"/>
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75 </valid>
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76 </sanitizer>
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77 <validator type="regex">[0-9a-zA-Z_]+</validator>
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78 </param>
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79 <param name="fasta" type="data" format="fasta,fasta.gz" label="Genome Sequence" help="Input genome"/>
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80 </repeat>
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81 <!-- add an option for root -->
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82 <!-- root mr -->
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83 </inputs>
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84 <outputs>
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85 <data name="out_hal" format="h5" from_work_dir="alignment.full.hal" label="${tool.name} on ${on_string} (HAL file)">
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86 </data>
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87 <data name="out_gfa" format="gfa2.gz" from_work_dir="alignment.gfa.gz" label="${tool.name} on ${on_string} (GFA file)">
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88 <filter>aln_mode['aln_mode_select'] == 'intraspecies'</filter>
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89 </data>
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90 </outputs>
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91 <tests>
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92 <!-- test interspecies mode -->
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93 <test expect_num_outputs="1">
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94 <conditional name="aln_mode">
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95 <param name="aln_mode_select" value="interspecies"/>
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96 <param name="in_tree" value="test_tree.nhx"/>
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97 </conditional>
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98 <repeat name="in_seqs">
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99 <param name="label" value="simCow_chr6"/>
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100 <param name="fasta" value="simCow_chr6.fasta"/>
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101 </repeat>
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102 <repeat name="in_seqs">
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103 <param name="label" value="simDog_chr6"/>
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104 <param name="fasta" value="simDog_chr6.fasta"/>
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105 </repeat>
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106 <repeat name="in_seqs">
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107 <param name="label" value="simHuman_chr6"/>
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108 <param name="fasta" value="simHuman_chr6.fasta"/>
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109 </repeat>
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110 <repeat name="in_seqs">
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111 <param name="label" value="simMouse_chr6"/>
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112 <param name="fasta" value="simMouse_chr6.fasta"/>
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113 </repeat>
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114 <repeat name="in_seqs">
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115 <param name="label" value="simRat_chr6"/>
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116 <param name="fasta" value="simRat_chr6.fasta"/>
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117 </repeat>
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118 <output name="out_hal">
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119 <assert_contents>
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120 <has_size value="4472551" delta="200000"/>
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121 </assert_contents>
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122 </output>
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123 </test>
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124 <!-- within-species mode -->
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125 <test expect_num_outputs="2">
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126 <conditional name="aln_mode">
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127 <param name="aln_mode_select" value="intraspecies"/>
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128 <param name="ref_level" value="simCow_chr6"/>
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129 </conditional>
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130 <repeat name="in_seqs">
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131 <param name="label" value="simCow_chr6"/>
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132 <param name="fasta" value="simCow_chr6.fasta"/>
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133 </repeat>
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134 <repeat name="in_seqs">
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135 <param name="label" value="simDog_chr6"/>
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136 <param name="fasta" value="simDog_chr6.fasta"/>
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137 </repeat>
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138 <repeat name="in_seqs">
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139 <param name="label" value="simHuman_chr6"/>
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140 <param name="fasta" value="simHuman_chr6.fasta"/>
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141 </repeat>
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142 <repeat name="in_seqs">
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143 <param name="label" value="simMouse_chr6"/>
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144 <param name="fasta" value="simMouse_chr6.fasta"/>
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145 </repeat>
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diff changeset
146 <repeat name="in_seqs">
51c3c42bc644 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus commit 827619d22d2931d8fb34ed6844cfa91433e1ac2c
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147 <param name="label" value="simRat_chr6"/>
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148 <param name="fasta" value="simRat_chr6.fasta"/>
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149 </repeat>
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150 <output name="out_hal">
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151 <assert_contents>
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152 <has_size value="565214" delta="65214"/>
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153 </assert_contents>
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154 </output>
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155 <output name="out_gfa">
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156 <assert_contents>
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157 <has_size value="173000" delta="200000"/>
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158 </assert_contents>
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159 </output>
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160 </test>
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161 <!-- FASTA header with spaces (used to fail) -->
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162 <test expect_num_outputs="2">
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163 <conditional name="aln_mode">
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164 <param name="aln_mode_select" value="intraspecies"/>
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165 <param name="ref_level" value="badheader1"/>
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166 </conditional>
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167 <repeat name="in_seqs">
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168 <param name="label" value="badheader1"/>
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169 <param name="fasta" value="bh1.fasta.gz"/>
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170 </repeat>
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171 <repeat name="in_seqs">
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diff changeset
172 <param name="label" value="badheader2"/>
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173 <param name="fasta" value="bh2.fasta.gz"/>
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174 </repeat>
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175 <output name="out_hal">
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176 <assert_contents>
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177 <has_size value="3382274" delta="200000"/>
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178 </assert_contents>
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179 </output>
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180 <output name="out_gfa">
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181 <assert_contents>
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182 <has_size value="764748" delta="200000"/>
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183 </assert_contents>
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184 </output>
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185 </test>
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186 </tests>
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187 <help><![CDATA[
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188
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189 .. class:: infomark
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190
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191 **What it does**
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192
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193 `Cactus <https://github.com/ComparativeGenomicsToolkit/cactus>`__ is a
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194 reference-free whole-genome multiple alignment program. It can be used
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195 to progressively align a large number of genomes.
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196
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197 -----
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198
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199 .. class:: infomark
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200
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201 **Usage**
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202
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203 **Between-species mode (Progressive Cactus)**
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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 **Within-species mode (Minigraph-Cactus)**
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220
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221 You can also run Cactus in `pangenome
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222 mode <https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md>`__
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223 to align genomes of multiple individuals from the **same species**. In
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224 this mode you will not use a guide tree. Cactus will use
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225 `minigraph <https://github.com/lh3/minigraph>`__ to generate a graph of
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226 the input genomes and then use the graph to order the alignments. To use
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227 pangenome mode, select ‘Within-species’ in the ‘Alignment mode’
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228 dropdown.
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229
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230 Unlike Between-species mode, Within-species mode depends on a predetermined reference genome.
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231
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232 -----
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233
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234 .. class:: infomark
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235
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236 **Input**
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237
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238 The developers recommend soft-masking your genomes with RepeatMasker
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239 before running Cactus. RepeatMasker is available on Galaxy.
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240
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241 If you’re using Between-species mode, you need to provide labels for the
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242 fasta files that match the leaves on the guide tree. In the example
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243 above, you would use the label ‘human’ for the human fasta file.
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244
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245 -----
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246
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247 .. class:: infomark
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248
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249 **Output**
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250
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251 The main output of Cactus is in `HAL
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252 format <https://github.com/ComparativeGenomicsToolkit/cactus#using-the-output>`__.
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253 You can use the `Cactus: export <root?tool_id=cactus_export>`__ tool to
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254 convert the Cactus output to a VG or Multiple Alignment Format (MAF)
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255 file.
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256
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257
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258 ]]></help>
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259 <expand macro="citations"/>
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260 </tool>