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annotate fasta-stats.xml @ 0:9c620a950d3a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
author iuc
date Thu, 22 Nov 2018 04:16:35 -0500
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children 16f1f3e2de42
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9c620a950d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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1 <tool id="fasta-stats" name="Fasta Statistics" version="1.0.1">
9c620a950d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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2 <description>Display summary statistics for a fasta file.</description>
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3 <requirements>
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4 <requirement type="package" version="5.26">perl</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 perl '${__tool_directory__}/fasta-stats.pl'
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8 '$dataset'
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9 > '$stats'
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10 ]]>
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11 </command>
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12 <inputs>
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13 <param name="dataset" type="data" format="fasta" label="fasta or multifasta file" help="fasta dataset to get statistics for."/>
9c620a950d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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14 </inputs>
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15 <outputs>
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16 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: Fasta summary stats"/>
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="dataset" value="test.fasta"/>
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21 <output name="stats" file="test_out.txt"/>
9c620a950d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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22 </test>
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23 </tests>
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24 <help>
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25 **Fasta Stats**
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26 Displays the summary statistics for a fasta file.
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27
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28 ------
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29
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30 Outputs in tabular form:
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31 Lengths: n50, min, max, median and average
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32
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33 Number of base pairs: A, C, G, T, N, Total and Total_not_N
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34
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35 Number of sequences
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36
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37 GC content in %
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38
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39 ------
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41 Inputs:
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42
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43 Fasta dataset
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44 </help>
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45 <citations>
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46 <citation type="bibtex">
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47 @UNPUBLISHED{Seemann_Gladman2012,
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48 author = {Torsten Seemann and Simon Gladman},
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49 title = {Fasta Statistics: Display summary statistics for a fasta file.},
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50 year = {2012},
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51 url = {https://github.com/galaxyproject/tools-iuc},
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52 }
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53 </citation>
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54 </citations>
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55 </tool>