Mercurial > repos > brinkmanlab > mauve_contig_mover

annotate mauve_contig_mover.xml @ 6:4931255f2fcc draft

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 25b7aeca541e258a2bff5d0e34e9298996b4a47b"
author brinkmanlab
date Fri, 20 Nov 2020 18:58:52 +0000
parents f8b09693c9c1
children 4c4838703fa8
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c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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1 <tool id="mauve-contig-mover" name="Mauve Contig Mover" version="1.0" profile="16.04">
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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2 <description>Reorder a multi-contig dataset against a reference genome</description>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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3 <edam_topics>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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4 <edam_topic>topic_0196</edam_topic>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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5 <edam_topic>topic_0091</edam_topic>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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6 </edam_topics>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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7 <edam_operations>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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8 <edam_operation>operation_0495</edam_operation>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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9 <edam_operation>operation_0491</edam_operation>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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10 </edam_operations>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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11 <requirements>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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12 <requirement type="package" version="2.4.0.snapshot_2015_02_13">mauve</requirement>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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13 </requirements>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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14 <version_command>mauveAligner --version</version_command>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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15 <command detect_errors="exit_code"><![CDATA[
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16 #if $ref_select.ref_source == "db"
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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17 #set global $index = $ref_select.ref_db
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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18 #else if $ref_select.ref_source == "meta"
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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19 #set global $index = $data.metadata.dbkey
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20 #else if $ref_select.ref_source == "key"
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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21 #set global $index = $ref_select.key
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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22 #else
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23 #set global $index = None
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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24 #set $ref = $ref_select.ref
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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25 #if $ref.is_of_type("genbank")
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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26 ln -sf $ref `basename $ref`.gbk &&
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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27 #set $ref = $os.path.basename(str($ref)) + ".gbk"
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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28 #end if
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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29 #end if
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30
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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31 #if $index
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32 ## Get path to database file
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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33 #try
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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34 #set $ref = next(record for record in $__app__.tool_data_tables['all_fasta'].get_fields() if str( record[1] ) == str( $index ))[-1]
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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35 #except StopIteration
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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36 #raise ValueError('Reference not found: '+str($index))
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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37 #end try
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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38 #end if
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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39
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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40 #if $draft.is_of_type("genbank")
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41 ln -sf $draft `basename ${draft}.gbk` &&
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42 #set $draft_path = $os.path.basename(str($draft)) + ".gbk"
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43 #else
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44 #set $draft_path = str($draft)
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45 #end if
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46
6
4931255f2fcc "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 25b7aeca541e258a2bff5d0e34e9298996b4a47b"
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47 test -r $ref && MauveCM -output output -ref $ref -draft $draft_path && $__tool_directory__/mcm_final.sh
0
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48 ]]></command>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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49 <inputs>
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50 <param name="draft" type="data" format="genbank,fasta" label="Draft" />
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51 <conditional name="ref_select">
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52 <param name="ref_source" type="select" label="Select the source of the reference to align the draft to">
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53 <option value="db">Data manager</option>
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54 <option value="file">History</option>
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55 <option value="meta" selected="true">Input Metadata</option>
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56 <option value="key">Key</option>
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57 </param>
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58 <when value="file">
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59 <param name="ref" type="data" format="genbank,fasta" label="Reference" />
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60 </when>
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61 <when value="db">
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62 <param name="ref_db" type="select" label="Using reference genome" help="Select genome from the list">
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63 <options from_data_table="all_fasta">
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64 <filter type="sort_by" column="2" />
5
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65 <column name="name" index="2" />
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66 <column name="value" index="1" />
0
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67 </options>
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68 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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69 </param>
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70 </when>
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71 <when value="meta">
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72 </when>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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73 <when value="key">
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74 <!-- this is a workaround until https://github.com/galaxyproject/galaxy/issues/7496 is resolved -->
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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75 <param name="key" type="text" label="Provide a dbkey to use" />
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76 </when>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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77 </conditional>
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78 </inputs>
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79 <outputs>
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80 <data name="reordered" format="fasta" from_work_dir="final.reordered" label="${tool.name} on ${on_string}: Reordered" />
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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81 <data name="backbone" format="tabular" from_work_dir="final.backbone" label="${tool.name} on ${on_string}: Backbone" />
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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82 <data name="contigs" format="tabular" from_work_dir="final.contigs.tab" label="${tool.name} on ${on_string}: Contig Order" />
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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83 <data name="features" format="tabular" from_work_dir="final.features.tab" label="${tool.name} on ${on_string}: Features">
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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84 <filter>hasattr(draft, 'is_of_type') and draft.is_of_type("genbank")</filter>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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85 </data>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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86 </outputs>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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87 <tests>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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88 <test expect_failure="true">
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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89 <!-- Mauve uses biojava which currently has a bug: https://github.com/biojava/biojava/issues/843 -->
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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90 <param name="draft" value="test-data/draft.gbff" ftype="genbank" />
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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91 <conditional name="ref_select">
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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92 <param name="ref_source" value="file" />
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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93 <param name="ref" value="test-data/ref.gbff" ftype="genbank" />
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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94 </conditional>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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95 </test>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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96 <test expect_num_outputs="4">
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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97 <param name="draft" value="test-data/draft_bioperl.gbff" ftype="genbank" />
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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98 <conditional name="ref_select">
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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99 <param name="ref_source" value="file" />
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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100 <param name="ref" value="test-data/ref_bioperl.gbff" ftype="genbank" />
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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101 </conditional>
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102 <output name="reordered" checksum="sha256:2a5e621227f4967337cefd68273f78d3390c94f5fd7ce4dcbf8024a342aeb976" ftype="fasta" />
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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103 <output name="backbone" checksum="sha256:f46966bcaed3324e43cad91161f380427a7d3cc52bbf823ae811d3f5dfaf2927" ftype="tabular" />
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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104 <output name="contigs" file="test-data/contig_order.tabular" ftype="tabular" />
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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105 <output name="features" checksum="sha256:e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855" ftype="tabular" />
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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106 </test>
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107 </tests>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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108 <help><![CDATA[
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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109 The Mauve Contig Mover (MCM) can be used to order a draft genome relative to a related reference genome.
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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110 The functionality of this software module has been described in Rissman et al. 2009, a publication in Bioinformatics.
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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111 The Mauve Contig Mover can ease a comparative study between draft and reference sequences by ordering draft contigs according to the reference genome.
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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112 In many cases, true rearrangements in the draft relative to the reference can be identified. The quality of the reorder is limited by the distance between
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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113 the sequences, as indicated by the amount of shared gene content among the two organisms. A more distant reference will usually yield fewer ordered draft genome contigs,
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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114 and may also induce erroneous placements of draft contigs. In addition to ordering contigs, MCM also orient them in the most likely orientation, and, if annotated sequence
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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115 features are specified in an input file (e.g. with GenBank format input for the draft), MCM will output adjusted coordinates ranges for the features.
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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116
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117 Outputs:
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118
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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119 "Backbone" is the backbone output by mauveAligner representing the alignements.
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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120
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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121 "Reordered" is a fasta file with the contigs reordered. Contigs aligned in reverse will be thier compliment sequence.
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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122
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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123 "Contig Order" acts as an index to the fasta as the contig orders and orientations change (even if the draft was originally
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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124 input as a genbank, after the first alignment, it will be converted to a fasta with annotation information preserved in a file described below).
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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125 The file is divided into 3 sections, each containing a list of contigs. The data for each contig includes its label (name),
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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126 its location in the genome (numbered in pseudocoordinates from the first to last contig, and whether it is oriented the same as originally input,
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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127 or was complemented.
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128
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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129 The three sections are described below:
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130
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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131 Contigs to reverse:
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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132 This section contains contigs whose order is reversed with respect to the previous iteration.
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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133 Note that contigs in this section may be oriented the same as originally input, this can be determined from the forward orcomplement designation.
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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134
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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135 Ordered Contings:
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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136 This is a list of all the contigs in the order and orientation they appear in the fasta for the draft of this iteration of the reorder.
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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137 Since these include all the contigs in the original input, those with no ordering information (no aligned region) will be clustered at the end.
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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138 These will appear as contigs with no LCBs at the end of the draft genome.
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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139
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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140 Contigs with Conflicting Order information:
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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141 This is a list of contigs containing LCBs suggesting multiple possible locations.
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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142 These may be of interest to verify positioning, or to look at points of potential rearrangement or misassembly.
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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143
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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144 If the draft was input as an annotated genbank file, a second file will appear called "Features". This file will contain a line for each annotation,
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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145 information about its current orientation and location (which will change if the contig is inverted), coordinates from the previous iteration (indicating
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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146 relative orientation), and whether it is reversed from the original input. It will also have a label field used to identify each feature.
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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147 This will be gotten from the annotation, as checked in the following order: db_xref, label, gene, and locus_tag.
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148 ]]></help>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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149 <citations>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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150 <citation type="doi">10.5281/zenodo.3364789</citation>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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151 <citation type="doi">10.1093/bioinformatics/btp356</citation>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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152 </citations>
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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153 </tool>