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annotate cactus_export.xml @ 14:3ff17bad4006 draft

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planemo upload for repository https://github.com/usegalaxy-au/tools-au commit af33e7925766b58ea176ec8f6a5729330ddd383f
author galaxy-australia
date Mon, 28 Aug 2023 23:09:49 +0000
parents d7ce0ec78e51
children c44f824c051a
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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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9 export TMPDIR=\${_GALAXY_JOB_TMP_DIR} &&
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11 ## check if the reference level was specified
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12 #if $export_select.format in ['maf_selector', 'vg_selector']:
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13 #if $export_select.ref_level == '':
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14 echo "You must provide a reference level" &&
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15 exit 1
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16 #end if
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17 #end if
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18
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19 ln -s '$hal_file' alignment.hal
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21 ## make a MAF
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22 #if $export_select.format == 'maf_selector':
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23 &&
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24 hal2maf
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25 --refGenome $export_select.ref_level
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26 alignment.hal
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27 alignment.maf
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28 #end if
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29
4
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30 ## make an assemblyHub
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31 #if $export_select.format == 'ah_selector':
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32 &&
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33 hal2assemblyHub.py
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34 --maxCores \${GALAXY_SLOTS:-4}
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35 --maxMemory \${GALAXY_MEMORY_MB:-8192}M
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36 ./jobStore
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37 alignment.hal
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38 assemblyhub
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39 &&
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40 tar -cv assemblyhub > assemblyhub.tar
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41 #end if
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42
4
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43 ## make a VG
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44 #if $export_select.format == 'vg_selector':
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45 &&
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46 hal2vg alignment.hal
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47 --progress
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48 > alignment.pg
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49 #end if
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50
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51 ]]></command>
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52 <inputs>
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53 <param name="hal_file" type="data" format="h5" label="HAL file" help="Multiple-genome alignment generated by Cactus" />
4
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54 <conditional name="export_select">
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55 <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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56 <option value="maf_selector" selected="true">MAF file</option>
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57 <option value="ah_selector">Assembly Hub</option>
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58 <option value="vg_selector">VG file</option>
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59 </param>
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60 <when value="maf_selector">
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61 <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'." />
0
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62 </when>
4
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63 <when value="ah_selector">
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64 </when>
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65 <when value="vg_selector">
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66 <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'." />
0
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67 </when>
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68 </conditional>
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69 </inputs>
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70 <outputs>
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71 <data name="out_maf" format="maf" from_work_dir="alignment.maf" label="${tool.name} on ${on_string} (MAF file)" >
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72 <filter>export_select['format'] == 'maf_selector'</filter>
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73 </data>
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74 <data name="out_vg" format="vg" from_work_dir="alignment.pg" label="${tool.name} on ${on_string} (VG file)" >
4
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75 <filter>export_select['format'] == 'vg_selector'</filter>
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76 </data>
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77 <data name="out_ah" format="tar" from_work_dir="assemblyhub.tar" label="${tool.name} on ${on_string} (Assembly Hub)" >
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78 <filter>export_select['format'] == 'ah_selector'</filter>
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79 </data>
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80 </outputs>
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81 <tests>
4
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82 <!-- this fails because no reference level is set -->
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83 <test expect_failure="true">
4
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84 <conditional name="export_select">
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85 <param name="format" value="maf_selector" />
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86 </conditional>
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87 <param name="hal_file" ftype="h5" value="evolverMammals.hal" />
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88 </test>
4
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89 <!-- within-species mode -->
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90 <test expect_num_outputs="1">
4
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91 <conditional name="export_select">
0
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92 <param name="ref_level" value="simMouse_chr6" />
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93 <param name="format" value="maf_selector" />
0
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94 </conditional>
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95 <param name="hal_file" ftype="h5" value="within.hal" />
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96 <output name="out_maf" file="set_reference.maf" />
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97 </test>
4
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98 <!-- between-species -->
0
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99 <test expect_num_outputs="1">
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galaxy-australia
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100 <conditional name="export_select">
0
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101 <param name="ref_level" value="simMouse_chr6" />
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102 <param name="format" value="maf_selector" />
0
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103 </conditional>
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104 <param name="hal_file" ftype="h5" value="evolverMammals_noroot.hal" />
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105 <output name="out_maf" file="evolverMammals_noroot.maf" />
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106 </test>
4
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107 <!-- assembly hub format -->
0
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108 <test expect_num_outputs="1">
4
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galaxy-australia
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109 <conditional name="export_select">
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110 <param name="format" value="ah_selector" />
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111 </conditional>
0
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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112 <param name="hal_file" ftype="h5" value="within.hal" />
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galaxy-australia
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113 <output name="out_ah">
0
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114 <assert_contents>
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115 <has_archive_member path="assemblyhub/hub.txt"/>
0
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116 </assert_contents>
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117 </output>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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118 </test>
4
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119 <!-- vg format -->
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120 <test expect_num_outputs="1">
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121 <conditional name="export_select">
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galaxy-australia
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122 <param name="format" value="vg_selector" />
0
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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123 <param name="ref_level" value="simMouse_chr6" />
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124 </conditional>
4
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galaxy-australia
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125 <param name="hal_file" ftype="h5" value="within.hal" />
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galaxy-australia
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126 <output name="out_vg">
0
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127 <assert_contents>
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128 <has_size value="860452" delta="200000" />
0
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129 </assert_contents>
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130 </output>
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131 </test>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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132 <!-- gfa format (gfa2): not implemented -->
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133 </tests>
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134 <help><![CDATA[
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135 **What it does**
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136
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137 Converts the HAL output from `Cactus whole-genome multiple sequence
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138 aligner <root?tool_id=cactus_cactus>`__ into other formats.
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139
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140 **Input**
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141
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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142 A `HAL
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143 file <https://github.com/ComparativeGenomicsToolkit/cactus#using-the-output>`__
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144 from `Cactus <root?tool_id=cactus_cactus>`__.
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145
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146 **Output**
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147
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148 Currently, you can export a pangenome in VG format, for use with
4
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149 `vg <https://github.com/vgteam/vg>`__, or Multiple Alignment Format
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150 (MAF). Note that these files are **reference-based**, so it will contain
0
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151 alignments to a single reference from your list of inputs (i.e. not a
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152 graph). You have to provide this with the ‘reference genome’ option.
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153
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154 You can also export an Assembly Hub for use with the UCSC Genome Browser.
0
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155 ]]></help>
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156 <expand macro="citations"/>
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157 </tool>