Mercurial > repos > brinkmanlab > mauve_contig_mover
annotate mauve_contig_mover.xml @ 0:c14690ec0c9f draft
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
author | brinkmanlab |
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date | Fri, 24 Jan 2020 17:43:19 -0500 |
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children | f8b09693c9c1 |
rev | line source |
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0
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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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"
brinkmanlab
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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"
brinkmanlab
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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"
brinkmanlab
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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"
brinkmanlab
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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"
brinkmanlab
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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"
brinkmanlab
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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"
brinkmanlab
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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"
brinkmanlab
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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"
brinkmanlab
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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"
brinkmanlab
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11 <requirements> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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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"
brinkmanlab
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13 </requirements> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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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"
brinkmanlab
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15 <command detect_errors="exit_code"><![CDATA[ |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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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"
brinkmanlab
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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"
brinkmanlab
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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"
brinkmanlab
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19 #set global $index = $data.metadata.dbkey |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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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"
brinkmanlab
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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"
brinkmanlab
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22 #else |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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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"
brinkmanlab
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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"
brinkmanlab
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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"
brinkmanlab
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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"
brinkmanlab
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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 |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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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 |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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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( $index ))[-1] |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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35 #except StopIteration |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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36 #raise ValueError('Reference not found: '+str($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"
brinkmanlab
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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"
brinkmanlab
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40 #if $draft.is_of_type("genbank") |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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41 ln -sf $draft `basename ${draft}.gbk` && |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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42 #set $draft_path = $os.path.basename(str($draft)) + ".gbk" |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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43 #else |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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44 #set $draft_path = str($draft) |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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45 #end if |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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46 |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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47 MauveCM -output output -ref $ref -draft $draft_path && $__tool_directory__/mcm_final.sh |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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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> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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50 <param name="draft" type="data" format="genbank,fasta" label="Draft" /> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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51 <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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52 <param name="ref_source" type="select" label="Select the source of the reference to align the draft to"> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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53 <option value="db">Data manager</option> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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54 <option value="file">History</option> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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55 <option value="meta" selected="true">Input Metadata</option> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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56 <option value="key">Key</option> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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57 </param> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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58 <when value="file"> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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59 <param name="ref" type="data" format="genbank,fasta" label="Reference" /> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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60 </when> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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61 <when value="db"> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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62 <param name="ref_db" type="select" label="Using reference genome" help="Select genome from the list"> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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63 <options from_data_table="all_fasta"> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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64 <filter type="sort_by" column="2" /> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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65 </options> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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66 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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67 </param> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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68 </when> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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69 <when value="meta"> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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70 </when> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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71 <when value="key"> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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72 <!-- 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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73 <param name="key" type="text" label="Provide a dbkey to use" /> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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74 </when> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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75 </conditional> |
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76 </inputs> |
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77 <outputs> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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78 <data name="reordered" format="fasta" from_work_dir="final.reordered" label="${tool.name} on ${on_string}: Reordered" /> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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79 <data name="backbone" format="tabular" from_work_dir="final.backbone" label="${tool.name} on ${on_string}: Backbone" /> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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80 <data name="contigs" format="tabular" from_work_dir="final.contigs.tab" label="${tool.name} on ${on_string}: Contig Order" /> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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81 <data name="features" format="tabular" from_work_dir="final.features.tab" label="${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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82 <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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83 </data> |
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84 </outputs> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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85 <tests> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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86 <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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87 <!-- 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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88 <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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89 <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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90 <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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91 <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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92 </conditional> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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93 </test> |
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94 <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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95 <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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96 <conditional name="ref_select"> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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97 <param name="ref_source" value="file" /> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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98 <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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99 </conditional> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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100 <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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101 <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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102 <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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103 <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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104 </test> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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105 </tests> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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106 <help><![CDATA[ |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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107 The Mauve Contig Mover (MCM) can be used to order a draft genome relative to a related reference genome. |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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108 The functionality of this software module has been described in Rissman et al. 2009, a publication in Bioinformatics. |
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"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 can ease a comparative study between draft and reference sequences by ordering draft contigs according to the reference genome. |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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110 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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111 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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112 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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113 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. |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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114 |
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115 Outputs: |
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116 |
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117 "Backbone" is the backbone output by mauveAligner representing the alignements. |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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118 |
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119 "Reordered" is a fasta file with the contigs reordered. Contigs aligned in reverse will be thier compliment sequence. |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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120 |
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121 "Contig Order" acts as an index to the fasta as the contig orders and orientations change (even if the draft was originally |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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122 input as a genbank, after the first alignment, it will be converted to a fasta with annotation information preserved in a file described below). |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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123 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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124 its location in the genome (numbered in pseudocoordinates from the first to last contig, and whether it is oriented the same as originally input, |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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125 or was complemented. |
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126 |
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127 The three sections are described below: |
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128 |
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129 Contigs to reverse: |
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130 This section contains contigs whose order is reversed with respect to the previous iteration. |
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131 Note that contigs in this section may be oriented the same as originally input, this can be determined from the forward orcomplement designation. |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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132 |
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133 Ordered Contings: |
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134 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. |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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135 Since these include all the contigs in the original input, those with no ordering information (no aligned region) will be clustered at the end. |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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136 These will appear as contigs with no LCBs at the end of the draft genome. |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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137 |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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138 Contigs with Conflicting Order information: |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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139 This is a list of contigs containing LCBs suggesting multiple possible locations. |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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140 These may be of interest to verify positioning, or to look at points of potential rearrangement or misassembly. |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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141 |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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142 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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143 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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144 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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145 This will be gotten from the annotation, as checked in the following order: db_xref, label, gene, and locus_tag. |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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146 ]]></help> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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147 <citations> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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148 <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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149 <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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150 </citations> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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151 </tool> |