Mercurial > repos > brinkmanlab > mauve_contig_mover
comparison mauve_contig_mover.xml @ 7:4c4838703fa8 draft default tip
planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit d396bc9f82b351c35ae4940ebfbb6a43e6e7215a
| author | brinkmanlab |
|---|---|
| date | Thu, 25 Aug 2022 21:03:33 +0000 |
| parents | 4931255f2fcc |
| children |
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| 6:4931255f2fcc | 7:4c4838703fa8 |
|---|---|
| 9 <edam_operation>operation_0491</edam_operation> | 9 <edam_operation>operation_0491</edam_operation> |
| 10 </edam_operations> | 10 </edam_operations> |
| 11 <requirements> | 11 <requirements> |
| 12 <requirement type="package" version="2.4.0.snapshot_2015_02_13">mauve</requirement> | 12 <requirement type="package" version="2.4.0.snapshot_2015_02_13">mauve</requirement> |
| 13 </requirements> | 13 </requirements> |
| 14 <version_command>mauveAligner --version</version_command> | 14 <version_command>progressiveMauve --version</version_command> |
| 15 <command detect_errors="exit_code"><![CDATA[ | 15 <command detect_errors="exit_code"><![CDATA[ |
| 16 #if $ref_select.ref_source == "db" | 16 #if $ref_select.ref_source == "db" |
| 17 #set global $index = $ref_select.ref_db | 17 #set global $index = $ref_select.ref_db |
| 18 #else if $ref_select.ref_source == "meta" | 18 #else if $ref_select.ref_source == "meta" |
| 19 #set global $index = $data.metadata.dbkey | 19 #set global $index = $data.metadata.dbkey |
| 42 #set $draft_path = $os.path.basename(str($draft)) + ".gbk" | 42 #set $draft_path = $os.path.basename(str($draft)) + ".gbk" |
| 43 #else | 43 #else |
| 44 #set $draft_path = str($draft) | 44 #set $draft_path = str($draft) |
| 45 #end if | 45 #end if |
| 46 | 46 |
| 47 test -r $ref && MauveCM -output output -ref $ref -draft $draft_path && $__tool_directory__/mcm_final.sh | 47 test -r $ref && MauveCM -output output -ref $ref -draft $draft_path && $__tool_directory__/mcm_final.sh || ( echo 'Invalid path ' $ref; exit 1 ) |
| 48 ]]></command> | 48 ]]></command> |
| 49 <inputs> | 49 <inputs> |
| 50 <param name="draft" type="data" format="genbank,fasta" label="Draft" /> | 50 <param name="draft" type="data" format="genbank,fasta" label="Draft" /> |
| 51 <conditional name="ref_select"> | 51 <conditional name="ref_select"> |
| 52 <param name="ref_source" type="select" label="Select the source of the reference to align the draft to"> | 52 <param name="ref_source" type="select" label="Select the source of the reference to align the draft to"> |