Mercurial > repos > iuc > fasta_stats

annotate fasta-stats.xml @ 4:0dbb995c7d35 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 50f5cce5a8c11001e2c59600a2b99a4243b6d06f"
author iuc
date Thu, 18 Nov 2021 20:56:57 +0000
parents 56022eb50bbd
children
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1 <tool id="fasta-stats" name="Fasta Statistics" version="2.0" profile="20.05">
0dbb995c7d35 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 50f5cce5a8c11001e2c59600a2b99a4243b6d06f"
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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="1.21.4">numpy</requirement>
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5 <requirement type="package" version="1.79">biopython</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
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8 python '${__tool_directory__}/fasta-stats.py'
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9 --fasta '$fasta'
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10 --stats_output '$stats_output'
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11 #if $gaps_option
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12 --gaps_output '$gaps_output'
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13 #end if
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14 #if $genome_size
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15 --genome_size $genome_size
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16 #end if
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17 ]]>
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18 </command>
9c620a950d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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19 <inputs>
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20 <param argument="--fasta" type="data" format="fasta" label="FASTA or Multi-FASTA file" help="FASTA dataset to get statistics."/>
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21 <param argument="--genome_size" type="integer" min="0" optional="true" label="Estimated genome size" help="This parameter is optional. If provided, it will be used for calculating the NG50 statistic." />
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22 <param argument="--gaps_option" type="boolean" truevalue="true" falsevalue="false" label="Generate gap stats"/>
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23 </inputs>
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24 <outputs>
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25 <data name="stats_output" format="tabular" label="${tool.name} on ${on_string}: summary stats"/>
0dbb995c7d35 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 50f5cce5a8c11001e2c59600a2b99a4243b6d06f"
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26 <data name="gaps_output" format="bed" label="${tool.name} on ${on_string}: Gap stats">
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27 <filter>gaps_option</filter>
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28 </data>
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29 </outputs>
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30 <tests>
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31 <test expect_num_outputs="1">
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32 <param name="fasta" value="test.fasta" ftype="fasta"/>
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33 <output name="stats_output" file="test_01.tab" ftype="tabular"/>
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34 </test>
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35 <!--Test gap options and NG50-->
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36 <test expect_num_outputs="2">
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37 <param name="fasta" value="ng50_input.fasta" ftype="fasta"/>
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38 <param name="gaps_option" value="true"/>
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39 <param name="genome_size" value="4000"/>
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40 <output name="stats_output" file="test_02.tab" ftype="tabular"/>
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41 <output name="gaps_output" file="test_02.bed" ftype="bed"/>
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42 </test>
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43 <!--Compare outputs with QUAST-->
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44 <test expect_num_outputs="1">
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45 <param name="fasta" value="test_long_sequence.fasta" ftype="fasta"/>
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46 <output name="stats_output" ftype="tabular">
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47 <assert_contents>
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48 <has_text text="8353"/>
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49 <has_text text="303889"/>
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50 <has_text text="22107"/>
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51 </assert_contents>
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52 </output>
1
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53 </test>
0
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54 </tests>
4
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55 <help><![CDATA[
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56
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57 .. class:: infomark
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58
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59 **Purpose**
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60
0dbb995c7d35 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 50f5cce5a8c11001e2c59600a2b99a4243b6d06f"
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61 Displays the summary statistics for a FASTA file.
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62
9c620a950d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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63 ------
9c620a950d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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64
4
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65 .. class:: infomark
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66
0dbb995c7d35 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 50f5cce5a8c11001e2c59600a2b99a4243b6d06f"
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67 **Outputs**
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68
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69 This tool generates two outputs: a general summary and an optional gap stats file.
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70
4
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71 The general summary includes the following information:
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72
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73 - Lengths: n50, min, max, median and average
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74 - Number of base pairs: A, C, G, T, N, Total and Total_not_N
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75 - Number of sequences
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76 - GC content
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77
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78 In addition the optional gap stats BED file includes the information about gaps localization.
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79 ]]>
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80 </help>
9c620a950d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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81 <citations>
9c620a950d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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82 <citation type="bibtex">
4
0dbb995c7d35 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 50f5cce5a8c11001e2c59600a2b99a4243b6d06f"
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83 @UNPUBLISHED{Anmol_Kyran2021,
0dbb995c7d35 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 50f5cce5a8c11001e2c59600a2b99a4243b6d06f"
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84 author = {Anmol Kyran},
0dbb995c7d35 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 50f5cce5a8c11001e2c59600a2b99a4243b6d06f"
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85 title = {Fasta Statistics: Display summary statistics for a fasta file.},
0dbb995c7d35 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 50f5cce5a8c11001e2c59600a2b99a4243b6d06f"
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86 year = {2021},
0dbb995c7d35 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 50f5cce5a8c11001e2c59600a2b99a4243b6d06f"
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87 url = {https://github.com/galaxyproject/tools-iuc},
0dbb995c7d35 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 50f5cce5a8c11001e2c59600a2b99a4243b6d06f"
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88 }
0
9c620a950d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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89 </citation>
9c620a950d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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90 </citations>
9c620a950d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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91 </tool>