Mercurial > repos > brinkmanlab > mauve_contig_mover
annotate mcm_stitch.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 |
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date | Thu, 25 Aug 2022 21:03:33 +0000 |
parents | 1e2b70ac2ad6 |
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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-stitch" name="Mauve Contig Mover - Stitch" 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>Concatenate multiple contigs, complementing reversed sequences and rewriting all feature coordinates</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"
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"
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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_3436</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_0232</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"
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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="3.7">python</requirement> |
1
1e2b70ac2ad6
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit a7380cf90205de589a64fe0105ea957402d62300"
brinkmanlab
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13 <requirement type="package" version="1.76">biopython</requirement> |
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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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14 </requirements> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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15 <version_command><![CDATA[ $__tool_directory__/stitch.py -v ]]></version_command> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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16 <command detect_errors="aggressive"><![CDATA[ |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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17 python $__tool_directory__/stitch.py |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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18 #if $seqid |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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19 -s '$seqid' |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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20 #else |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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21 -s '$draft.element_identifier.replace(" ", "_")' |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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22 #end if |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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23 $pad_len $draft $draft.ext |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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24 #if $contigs |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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25 $contigs |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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26 #end if |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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27 > $output |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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28 ]]></command> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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29 <inputs> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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30 <param name="draft" type="data" format="abi,abi-trim,ace,cif-atom,cif-seqres,clustal,embl,fasta,fasta-2line,fastq-sanger,fastq,fastq-solexa,fastq-illumina,genbank,gb,ig,imgt,nexus,pdb-seqres,pdb-atom,phd,phylip,pir,seqxml,sff,sff-trim,stockholm,swiss,tab,qual,uniprot-xml,gff3" label="Draft" /> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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31 <param name="contigs" type="data" format="tabular" label="Contigs" optional="true" help="Contigs output from Mauve Contig Mover" /> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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32 <param name="pad_len" type="integer" min="0" value="1000" label="Pad length" help="Specify the length of padding to put between contigs" /> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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33 <param name="seqid" type="text" value="" label="Stitched sequence ID" help="Specify an ID to use for the stitched record, the dataset ID is used otherwise" /> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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34 </inputs> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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35 <outputs> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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36 <data name="output" format_source="draft" /> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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37 </outputs> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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38 <tests> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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39 <test expect_num_outputs="1"> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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40 <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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41 <param name="contigs" value="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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42 <output name="output" checksum="sha256:08afe06a0f1eb96aa7f2a5b9e8a5ca15a4775c884f3144b6d82f2a0668cdb210" ftype="genbank" /> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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43 </test> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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44 </tests> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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45 <help><![CDATA[ |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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46 Stitch contigs into a single contig. |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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47 Compliments reversed sequences and rewrites all feature coordinates. |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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48 For gankbank and embl, 'source' features are combined. |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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49 ]]></help> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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50 <citations> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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51 <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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52 </citations> |
c14690ec0c9f
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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53 </tool> |