Mercurial > repos > brinkmanlab > mauve_contig_mover
comparison mcm_stitch.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 |
parents | |
children | 1e2b70ac2ad6 |
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1 <tool id="mauve-contig-mover-stitch" name="Mauve Contig Mover - Stitch" version="1.0" profile="16.04"> | |
2 <description>Concatenate multiple contigs, complementing reversed sequences and rewriting all feature coordinates</description> | |
3 <edam_topics> | |
4 <edam_topic>topic_0196</edam_topic> | |
5 <edam_topic>topic_0091</edam_topic> | |
6 </edam_topics> | |
7 <edam_operations> | |
8 <edam_operation>operation_3436</edam_operation> | |
9 <edam_operation>operation_0232</edam_operation> | |
10 </edam_operations> | |
11 <requirements> | |
12 <requirement type="package" version="3.7">python</requirement> | |
13 <requirement type="package" version="1.73">biopython</requirement> | |
14 </requirements> | |
15 <version_command><![CDATA[ $__tool_directory__/stitch.py -v ]]></version_command> | |
16 <command detect_errors="aggressive"><![CDATA[ | |
17 python $__tool_directory__/stitch.py | |
18 #if $seqid | |
19 -s '$seqid' | |
20 #else | |
21 -s '$draft.element_identifier.replace(" ", "_")' | |
22 #end if | |
23 $pad_len $draft $draft.ext | |
24 #if $contigs | |
25 $contigs | |
26 #end if | |
27 > $output | |
28 ]]></command> | |
29 <inputs> | |
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" /> | |
31 <param name="contigs" type="data" format="tabular" label="Contigs" optional="true" help="Contigs output from Mauve Contig Mover" /> | |
32 <param name="pad_len" type="integer" min="0" value="1000" label="Pad length" help="Specify the length of padding to put between contigs" /> | |
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" /> | |
34 </inputs> | |
35 <outputs> | |
36 <data name="output" format_source="draft" /> | |
37 </outputs> | |
38 <tests> | |
39 <test expect_num_outputs="1"> | |
40 <param name="draft" value="test-data/draft_bioperl.gbff" ftype="genbank" /> | |
41 <param name="contigs" value="test-data/contig_order.tabular" ftype="tabular" /> | |
42 <output name="output" checksum="sha256:08afe06a0f1eb96aa7f2a5b9e8a5ca15a4775c884f3144b6d82f2a0668cdb210" ftype="genbank" /> | |
43 </test> | |
44 </tests> | |
45 <help><![CDATA[ | |
46 Stitch contigs into a single contig. | |
47 Compliments reversed sequences and rewrites all feature coordinates. | |
48 For gankbank and embl, 'source' features are combined. | |
49 ]]></help> | |
50 <citations> | |
51 <citation type="doi">10.5281/zenodo.3364789</citation> | |
52 </citations> | |
53 </tool> |