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annotate fasta-stats.xml @ 3:56022eb50bbd draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit ecd37d0702cbe5cf9fa244c129a008b039d5e164"
author iuc
date Mon, 05 Jul 2021 13:36:26 +0000
parents cd0874854f51
children 0dbb995c7d35
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56022eb50bbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit ecd37d0702cbe5cf9fa244c129a008b039d5e164"
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1 <tool id="fasta-stats" name="Fasta Statistics" version="1.0.3">
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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 #if $genome_size:
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10 $genome_size
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11 #end if
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12 > '$stats'
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13 ]]>
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14 </command>
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15 <inputs>
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16 <param name="dataset" type="data" format="fasta" label="fasta or multifasta file" help="fasta dataset to get statistics for."/>
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17 <param name="genome_size" type="float" optional="True" label="Genome size estimate (optional)" help="Estimate of the genome size in bases. If specified, NG50 and LG50 will be calculated."/>
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18 </inputs>
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19 <outputs>
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20 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: Fasta summary stats"/>
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="dataset" value="test.fasta"/>
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25 <output name="stats" file="test_out.txt"/>
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26 </test>
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27 <test>
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28 <param name="dataset" value="ng50_input.fasta"/>
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29 <param name="genome_size" value="4000"/>
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30 <output name="stats" file="ng50_out.txt"/>
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31 </test>
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32 </tests>
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33 <help>
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34 **Fasta Stats**
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35 Displays the summary statistics for a fasta file.
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36
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37 ------
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38
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39 Outputs in tabular form:
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40 Lengths: n50, min, max, median and average
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41
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42 Number of base pairs: A, C, G, T, N, Total and Total_not_N
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43
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44 Number of sequences
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45
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46 GC content in %
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47
1
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48 If an optional genome size estimate is specified, then the NG50 length will also be calculated.
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49
0
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50 ------
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51
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52 Inputs:
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53
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54 Fasta dataset
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55 </help>
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56 <citations>
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57 <citation type="bibtex">
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58 @UNPUBLISHED{Seemann_Gladman2012,
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59 author = {Torsten Seemann and Simon Gladman},
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60 title = {Fasta Statistics: Display summary statistics for a fasta file.},
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61 year = {2012},
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62 url = {https://github.com/galaxyproject/tools-iuc},
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63 }
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64 </citation>
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65 </citations>
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66 </tool>