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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 669399887aebfe546eae29022f446664d9b52d44"
author brinkmanlab
date Sat, 05 Sep 2020 04:20:01 +0000
parents f2656e644641
children
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a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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1 <tool id="make-unique-id" name="BioPython Make Unique ID" version="1.0" profile="16.04">
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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2 <description>Makes all record ids unique across all input data</description>
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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3 <edam_topics>
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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4 <edam_topic>topic_3345</edam_topic>
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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5 <edam_topic>topic_3489</edam_topic>
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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6 <edam_topic>topic_0091</edam_topic>
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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7 </edam_topics>
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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8 <edam_operations>
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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9 <edam_operation>operation_3282</edam_operation>
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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10 </edam_operations>
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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11 <requirements>
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f2656e644641 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit e3bef6bd24b0d0bf5645a5d1083c1fa886c19e4a"
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12 <requirement type="package" version="1.76">biopython</requirement>
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a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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13 </requirements>
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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14 <version_command><![CDATA[ python $__tool_directory__/make_unique_id.py -v ]]></version_command>
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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15 <command detect_errors="aggressive"><![CDATA[
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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16 python $__tool_directory__/make_unique_id.py ${inputs[0].ext}
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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17 #for $input, $output in $zip($inputs, $outputs)
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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18 $input $output
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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19 #end for
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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20 ]]></command>
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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21 <inputs>
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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22 <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" />
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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23 </inputs>
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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24 <outputs>
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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25 <collection name="outputs" type="list" structured_like="inputs" inherit_format="true" />
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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26 </outputs>
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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27 <tests>
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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28 <test expect_num_outputs="1">
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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29 <param name="inputs" >
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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30 <collection type="list">
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31 <element name="test1" value="test-data/1.fastq" ftype="fastq" />
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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32 <element name="test2" value="test-data/1.fastq" ftype="fastq" />
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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33 <element name="test3" value="test-data/1.fastq" ftype="fastq" />
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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34 </collection>
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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35 </param>
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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36 <output_collection name="outputs" type="list" count="3">
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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37 <element name="test1" ftype="fastq" checksum="TODO" />
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38 <element name="test2" ftype="fastq" checksum="TODO" />
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39 <element name="test3" ftype="fastq" checksum="TODO" />
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40 </output_collection>
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41 </test>
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42 </tests>
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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43 <help><![CDATA[
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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44 Ensure record IDs are unique across datasets.
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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45 Can read/write any formats supported by BioPython SeqIO.
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46
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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47 This is useful when aggregating data downstream and you want to ensure that there are no ID collisions.
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48 ]]></help>
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49 <citations>
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50 <citation type="doi">10.5281/zenodo.3364789</citation>
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51 </citations>
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52 </tool>