Mercurial > repos > brinkmanlab > make_unique_id
comparison make_unique_id.xml @ 0:a3a09dd8d09a draft
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
author | brinkmanlab |
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date | Fri, 24 Jan 2020 17:38:28 -0500 |
parents | |
children | f2656e644641 |
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1 <tool id="make-unique-id" name="BioPython Make Unique ID" version="1.0" profile="16.04"> | |
2 <description>Makes all record ids unique across all input data</description> | |
3 <edam_topics> | |
4 <edam_topic>topic_3345</edam_topic> | |
5 <edam_topic>topic_3489</edam_topic> | |
6 <edam_topic>topic_0091</edam_topic> | |
7 </edam_topics> | |
8 <edam_operations> | |
9 <edam_operation>operation_3282</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[ python $__tool_directory__/make_unique_id.py -v ]]></version_command> | |
16 <command detect_errors="aggressive"><![CDATA[ | |
17 python $__tool_directory__/make_unique_id.py ${inputs[0].ext} | |
18 #for $input, $output in $zip($inputs, $outputs) | |
19 $input $output | |
20 #end for | |
21 ]]></command> | |
22 <inputs> | |
23 <param name="inputs" type="data_collection" format="clustal,embl,fasta,fasta-2line,fastq-sanger,fastq,fastq-solexa,fastq-illumina,genbank,gb,imgt,nexus,phd,phylip,pir,seqxml,sff,stockholm,tab,qual" label="Input" /> | |
24 </inputs> | |
25 <outputs> | |
26 <collection name="outputs" type="list" structured_like="inputs" inherit_format="true" /> | |
27 </outputs> | |
28 <tests> | |
29 <test expect_num_outputs="1"> | |
30 <param name="inputs" > | |
31 <collection type="list"> | |
32 <element name="test1" value="test-data/1.fastq" ftype="fastq" /> | |
33 <element name="test2" value="test-data/1.fastq" ftype="fastq" /> | |
34 <element name="test3" value="test-data/1.fastq" ftype="fastq" /> | |
35 </collection> | |
36 </param> | |
37 <output_collection name="outputs" type="list" count="3"> | |
38 <element name="test1" ftype="fastq" checksum="TODO" /> | |
39 <element name="test2" ftype="fastq" checksum="TODO" /> | |
40 <element name="test3" ftype="fastq" checksum="TODO" /> | |
41 </output_collection> | |
42 </test> | |
43 </tests> | |
44 <help><![CDATA[ | |
45 Ensure record IDs are unique across datasets. | |
46 Can read/write any formats supported by BioPython SeqIO. | |
47 | |
48 This is useful when aggregating data downstream and you want to ensure that there are no ID collisions. | |
49 ]]></help> | |
50 <citations> | |
51 <citation type="doi">10.5281/zenodo.3364789</citation> | |
52 </citations> | |
53 </tool> |