Mercurial > repos > brinkmanlab > make_unique_id
diff 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 |
---|---|
date | Fri, 24 Jan 2020 17:38:28 -0500 |
parents | |
children | f2656e644641 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/make_unique_id.xml Fri Jan 24 17:38:28 2020 -0500 @@ -0,0 +1,53 @@ +<tool id="make-unique-id" name="BioPython Make Unique ID" version="1.0" profile="16.04"> + <description>Makes all record ids unique across all input data</description> + <edam_topics> + <edam_topic>topic_3345</edam_topic> + <edam_topic>topic_3489</edam_topic> + <edam_topic>topic_0091</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_3282</edam_operation> + </edam_operations> + <requirements> + <requirement type="package" version="3.7">python</requirement> + <requirement type="package" version="1.73">biopython</requirement> + </requirements> + <version_command><![CDATA[ python $__tool_directory__/make_unique_id.py -v ]]></version_command> + <command detect_errors="aggressive"><![CDATA[ + python $__tool_directory__/make_unique_id.py ${inputs[0].ext} + #for $input, $output in $zip($inputs, $outputs) + $input $output + #end for + ]]></command> + <inputs> + <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" /> + </inputs> + <outputs> + <collection name="outputs" type="list" structured_like="inputs" inherit_format="true" /> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="inputs" > + <collection type="list"> + <element name="test1" value="test-data/1.fastq" ftype="fastq" /> + <element name="test2" value="test-data/1.fastq" ftype="fastq" /> + <element name="test3" value="test-data/1.fastq" ftype="fastq" /> + </collection> + </param> + <output_collection name="outputs" type="list" count="3"> + <element name="test1" ftype="fastq" checksum="TODO" /> + <element name="test2" ftype="fastq" checksum="TODO" /> + <element name="test3" ftype="fastq" checksum="TODO" /> + </output_collection> + </test> + </tests> + <help><![CDATA[ + Ensure record IDs are unique across datasets. + Can read/write any formats supported by BioPython SeqIO. + + This is useful when aggregating data downstream and you want to ensure that there are no ID collisions. + ]]></help> + <citations> + <citation type="doi">10.5281/zenodo.3364789</citation> + </citations> +</tool>