Mercurial > repos > galaxy-australia > cactus_export

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus commit 8fc43fe1e8c12438a14dbd174a8af3e7cb8b55dc
author iuc
date Thu, 08 Feb 2024 08:52:41 +0000
parents d7ce0ec78e51
children
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c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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1 <tool id="cactus_export" name="Cactus: export" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
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2 <description>whole-genome multiple sequence alignment to other formats</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"/>
c18157c68134 "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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10 ## check if the reference level was specified
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11 #if $export_select.format in ['maf_selector', 'vg_selector']:
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12 #if $export_select.ref_level == '':
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13 echo "You must provide a reference level" &&
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14 exit 1 ;
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15 #end if
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16 #end if
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17
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18 ln -s '$hal_file' alignment.hal
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20 ## make a MAF
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21 #if $export_select.format == 'maf_selector':
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22 &&
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23 hal2maf
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24 --refGenome $export_select.ref_level
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25 alignment.hal
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26 alignment.maf
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27 #end if
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28
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29 ## make an assemblyHub
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30 #if $export_select.format == 'ah_selector':
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31 &&
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32 hal2assemblyHub.py
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33 --maxCores \${GALAXY_SLOTS:-4}
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34 --maxMemory \${GALAXY_MEMORY_MB:-8196}M
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35 ./jobStore
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36 alignment.hal
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37 assemblyhub
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38 &&
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39 tar -cv assemblyhub > assemblyhub.tar
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40 #end if
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41
4
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42 ## make a VG
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43 #if $export_select.format == 'vg_selector':
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44 &&
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45 hal2vg alignment.hal
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46 --progress
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47 > alignment.pg
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48 #end if
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49
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50 ]]></command>
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51 <inputs>
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52 <param name="hal_file" type="data" format="h5" label="HAL file" help="Multiple-genome alignment generated by Cactus"/>
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53 <conditional name="export_select">
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54 <param name="format" type="select" label="Output format" help="The type of output you want to export. Run this tool once for each output format.">
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55 <option value="maf_selector" selected="true">MAF file</option>
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56 <option value="ah_selector">Assembly Hub</option>
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57 <option value="vg_selector">VG file</option>
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58 </param>
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59 <when value="maf_selector">
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60 <param name="ref_level" type="text" value="" label="Reference genome" help="Specify one of the Input Genomes as the reference level. This must match the label used in 'Genome Label'."/>
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61 </when>
4
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62 <when value="ah_selector">
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63 </when>
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64 <when value="vg_selector">
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65 <param name="ref_level" type="text" value="" label="Reference genome" help="Specify one of the Input Genomes as the reference level. This must match the label used in 'Genome Label'."/>
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66 </when>
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67 </conditional>
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68 </inputs>
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69 <outputs>
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70 <data name="out_maf" format="maf" from_work_dir="alignment.maf" label="${tool.name} on ${on_string} (MAF file)">
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71 <filter>export_select['format'] == 'maf_selector'</filter>
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72 </data>
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73 <data name="out_vg" format="vg" from_work_dir="alignment.pg" label="${tool.name} on ${on_string} (VG file)">
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74 <filter>export_select['format'] == 'vg_selector'</filter>
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75 </data>
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76 <data name="out_ah" format="tar" from_work_dir="assemblyhub.tar" label="${tool.name} on ${on_string} (Assembly Hub)">
4
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77 <filter>export_select['format'] == 'ah_selector'</filter>
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78 </data>
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79 </outputs>
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80 <tests>
4
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81 <!-- this fails because no reference level is set -->
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82 <test expect_failure="true">
4
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83 <conditional name="export_select">
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84 <param name="format" value="maf_selector"/>
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85 </conditional>
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86 <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/evolverMammals.hal"/>
0
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87 </test>
4
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88 <!-- within-species mode -->
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89 <test expect_num_outputs="1">
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90 <conditional name="export_select">
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91 <param name="ref_level" value="simMouse_chr6"/>
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92 <param name="format" value="maf_selector"/>
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93 </conditional>
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94 <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/within.hal"/>
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95 <output name="out_maf" location="https://zenodo.org/record/8336793/files/set_reference.maf"/>
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96 </test>
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97 <!-- between-species -->
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98 <test expect_num_outputs="1">
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99 <conditional name="export_select">
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100 <param name="ref_level" value="simMouse_chr6"/>
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101 <param name="format" value="maf_selector"/>
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102 </conditional>
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103 <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/evolverMammals_noroot.hal"/>
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104 <output name="out_maf" location="https://zenodo.org/record/8336793/files/evolverMammals_noroot.maf"/>
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105 </test>
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106 <!-- assembly hub format -->
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107 <test expect_num_outputs="1">
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108 <conditional name="export_select">
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109 <param name="format" value="ah_selector"/>
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110 </conditional>
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111 <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/within.hal"/>
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112 <output name="out_ah">
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113 <assert_contents>
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114 <has_archive_member path="assemblyhub/hub.txt"/>
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115 </assert_contents>
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116 </output>
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117 </test>
4
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118 <!-- vg format -->
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119 <test expect_num_outputs="1">
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120 <conditional name="export_select">
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121 <param name="format" value="vg_selector"/>
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122 <param name="ref_level" value="simMouse_chr6"/>
0
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123 </conditional>
15
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124 <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/within.hal"/>
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125 <output name="out_vg">
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126 <assert_contents>
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127 <has_size value="860452" delta="200000"/>
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128 </assert_contents>
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129 </output>
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130 </test>
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131 <!-- gfa format (gfa2): not implemented -->
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132 </tests>
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133 <help><![CDATA[
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134 **What it does**
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135
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136 Converts the HAL output from `Cactus whole-genome multiple sequence
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137 aligner <root?tool_id=cactus_cactus>`__ into other formats.
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138
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139 **Input**
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140
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141 A `HAL
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142 file <https://github.com/ComparativeGenomicsToolkit/cactus#using-the-output>`__
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143 from `Cactus <root?tool_id=cactus_cactus>`__.
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144
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145 **Output**
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146
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147 Currently, you can export a pangenome in VG format, for use with
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148 `vg <https://github.com/vgteam/vg>`__, or Multiple Alignment Format
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149 (MAF). Note that these files are **reference-based**, so it will contain
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150 alignments to a single reference from your list of inputs (i.e. not a
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151 graph). You have to provide this with the ‘reference genome’ option.
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152
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153 You can also export an Assembly Hub for use with the UCSC Genome Browser.
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154 ]]></help>
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155 <expand macro="citations"/>
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156 </tool>