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annotate fasta_header_converter.xml @ 2:7ea4df039a53 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 978a8efb9969646b97873d69348971860f2793f5
author earlhaminst
date Wed, 22 Feb 2017 05:48:02 -0500
parents 4f9e5110914b
children dd268de3a107
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4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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1 <tool id="fasta_header_converter" name="FASTA header converter" version="0.1.1">
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
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2 <description>to append species information</description>
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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3 <command>
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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4 <![CDATA[
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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5 python '$__tool_directory__/fasta_header_converter.py'
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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6 -f '$fastaFile'
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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7 -j '$genesFile'
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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8 > '$outputFile'
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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9 ]]>
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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10 </command>
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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11 <inputs>
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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12 <param name="fastaFile" type="data" format="fasta" label="FASTA file" help="FASTA file with transcript ID as FASTA ID" />
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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13 <param name="genesFile" type="data" format="json" label="Gene feature information" help="In JSON format" />
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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14 </inputs>
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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15 <outputs>
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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16 <data format="fasta" name="outputFile" label="${tool.name} on ${on_string}" />
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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17 </outputs>
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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18 <tests>
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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19 <test>
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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20 <param name="fastaFile" ftype="nhx" value="test.fasta" />
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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21 <param name="genesFile" ftype="json" value="test.json" />
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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22 <output name="outputFile" file="out.fasta" />
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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23 </test>
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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24 </tests>
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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25 <help>
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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26 <![CDATA[
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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27 Simple converter for FASTA files, which appends the species name to the FASTA header for usage in TreeBeST. It uses gene feature information in JSON format (similar to the result of Ensembl REST API - lookup/id).
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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28 ]]>
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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29 </help>
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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30 <citations>
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
earlhaminst
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31 </citations>
4f9e5110914b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty
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32 </tool>