Mercurial > repos > brinkmanlab > make_unique_id
annotate make_unique_id.xml @ 1:061c3402a977 draft
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit b661895b5e2dff7235eb32476602c3b93411a42e"
author | brinkmanlab |
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date | Mon, 15 Jun 2020 18:48:27 -0400 |
parents | a3a09dd8d09a |
children | f2656e644641 |
rev | line source |
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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> |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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12 <requirement type="package" version="3.7">python</requirement> |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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13 <requirement type="package" version="1.73">biopython</requirement> |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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14 </requirements> |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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15 <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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16 <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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17 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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18 #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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19 $input $output |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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20 #end for |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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21 ]]></command> |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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22 <inputs> |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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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" /> |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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24 </inputs> |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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25 <outputs> |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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26 <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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27 </outputs> |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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28 <tests> |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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29 <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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30 <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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31 <collection type="list"> |
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="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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33 <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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34 <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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35 </collection> |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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36 </param> |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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37 <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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38 <element name="test1" ftype="fastq" checksum="TODO" /> |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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39 <element name="test2" ftype="fastq" checksum="TODO" /> |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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40 <element name="test3" ftype="fastq" checksum="TODO" /> |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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41 </output_collection> |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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42 </test> |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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43 </tests> |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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44 <help><![CDATA[ |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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45 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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46 Can read/write any formats supported by BioPython SeqIO. |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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47 |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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48 This is useful when aggregating data downstream and you want to ensure that there are no ID collisions. |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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49 ]]></help> |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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50 <citations> |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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51 <citation type="doi">10.5281/zenodo.3364789</citation> |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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52 </citations> |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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53 </tool> |