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annotate cactus_export.xml @ 2:2e093badc689 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 00:19:37 +0000
parents c18157c68134
children 5bf688a3ee2c
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c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
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1 <tool id="cactus_export" name="Cactus: export" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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2 <description>whole-genome multiple sequence alignment to other formats.</description>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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3 <macros>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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4 <import>macros.xml</import>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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5 </macros>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
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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"/>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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8 <command detect_errors="exit_code"><![CDATA[
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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9 ln -s '$hal_file' alignment.hal
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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10
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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11 ## make a MAF
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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12
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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13 #if $enable_maf.maf_selector:
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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14 &&
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
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15 hal2maf alignment.hal
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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16 #if str($enable_maf.ref_level):
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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17 --refGenome $enable_maf.ref_level
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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18 #end if
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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19 alignment.maf
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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20 #end if
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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21
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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22 ## make a VG
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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23
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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24 #if $vg_selector:
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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25 &&
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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26 hal2vg alignment.hal
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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27 --hdf5InMemory
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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28 --chop 32
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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29 --progress
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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30 > alignment.pg
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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31 #end if
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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32
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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33 ]]></command>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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34 <inputs>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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35 <param name="hal_file" type="data" format="h5" label="HAL file" help="Multiple-genome alignment generated by Cactus" />
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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36 <conditional name="enable_maf">
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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37 <param name="maf_selector" type="boolean" checked="false" label="Generate a MAF file" />
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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38 <when value="true">
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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39 <param name="ref_level" type="text" optional="True" value="" label="Optional: reference genome for MAF" help="Specify one of the Input Genomes as the reference level for the Multiple Alignment Format (MAF) file. This must match the label used in 'Genome Label'. If nothing is specified, the first Input Genome will be the reference genome in the MAF file. This option doesn't affect the HAL output." />
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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40 </when>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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41 <when value="false">
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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42 </when>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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43 </conditional>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
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44 <param name="vg_selector" type="boolean" checked="false" label="Generate a VG file" />
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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45 </inputs>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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46 <outputs>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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47 <data name="out_maf" format="maf" from_work_dir="alignment.maf" label="${tool.name} on ${on_string} (MAF file)" >
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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48 <filter>enable_maf['maf_selector']</filter>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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49 </data>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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50 <data name="out_vg" format="vg" from_work_dir="alignment.pg" label="${tool.name} on ${on_string} (VG file)" >
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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51 <filter>vg_selector</filter>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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52 </data>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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53 </outputs>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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54 <tests>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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55 <!-- within-species mode -->
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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56 <test expect_num_outputs="1">
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
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57 <conditional name="enable_maf">
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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58 <param name="maf_selector" value="true" />
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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59 </conditional>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
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60 <param name="hal_file" ftype="h5" value="evolverMammals.hal" />
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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61 <output name="out_maf" file="hal2maf.maf" />
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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62 </test>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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63 <!-- set reference level -->
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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64 <test expect_num_outputs="1">
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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65 <conditional name="enable_maf">
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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66 <param name="maf_selector" value="true" />
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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67 <param name="ref_level" value="simMouse_chr6" />
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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68 </conditional>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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69 <param name="hal_file" ftype="h5" value="within.hal" />
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
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70 <output name="out_maf" file="set_reference.maf" />
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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71 </test>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
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72 <!-- between-species, select reference level -->
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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73 <test expect_num_outputs="1">
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
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74 <conditional name="enable_maf">
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
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75 <param name="maf_selector" value="true" />
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
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76 <param name="ref_level" value="simMouse_chr6" />
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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77 </conditional>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
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78 <param name="hal_file" ftype="h5" value="evolverMammals_noroot.hal" />
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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79 <output name="out_maf" file="evolverMammals_noroot.maf" />
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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80 </test>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
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81 <!-- vg format -->
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
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82 <test expect_num_outputs="1">
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
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83 <param name="vg_selector" value="true" />
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
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84 <param name="hal_file" ftype="h5" value="within.hal" />
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
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85 <output name="out_vg">
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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86 <assert_contents>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
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87 <has_size value="3586577" delta="200000" />
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
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88 </assert_contents>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
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89 </output>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
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90 </test>
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
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91 <!-- vg and maf with reference level -->
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
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92 <test expect_num_outputs="2">
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
parents:
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93 <conditional name="enable_maf">
c18157c68134 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
galaxy-australia
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94 <param name="maf_selector" value="true" />
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95 <param name="ref_level" value="simMouse_chr6" />
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96 </conditional>
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97 <param name="vg_selector" value="true" />
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98 <param name="hal_file" ftype="h5" value="evolverMammals_noroot.hal" />
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99 <output name="out_maf" file="evolverMammals_both.maf" />
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100 <output name="out_vg" >
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101 <assert_contents>
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102 <has_size value="53055101" delta="200000" />
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103 </assert_contents>
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104 </output>
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105 </test>
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106 <!-- gfa format (gfa2): not implemented -->
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107 </tests>
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108 <help><![CDATA[
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109 **What it does**
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110
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111 Converts the HAL output from `Cactus whole-genome multiple sequence
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112 aligner <root?tool_id=cactus_cactus>`__ into other formats.
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113
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114 **Input**
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115
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116 A `HAL
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117 file <https://github.com/ComparativeGenomicsToolkit/cactus#using-the-output>`__
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118 from `Cactus <root?tool_id=cactus_cactus>`__.
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119
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120 **Output**
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121
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122 Currently, you can export a pangenome in VG format, for use with
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123 `vg <https://github.com/vgteam/vg>`__, and/or Multiple Alignment Format
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124 (MAF). Note that MAF is **reference-based**, so it will contain
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125 alignments to a single reference from your list of inputs (i.e. not a
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126 graph). By default, the first input genome will be used as the
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127 reference. You can override this with the ‘reference genome’ option.
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128 ]]></help>
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129 <expand macro="citations"/>
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130 </tool>