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annotate bandage_info.xml @ 5:d8b1027d6ce0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 7823462e83ff5efbcfd3161f7d471fd07da51611"
author iuc
date Sun, 12 Sep 2021 08:13:13 +0000
parents b2860df42e16
children b9e31c5c01c7
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1 <tool id="bandage_info" name="Bandage Info" version="@TOOL_VERSION@+galaxy2" profile="18.01">
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2 <description>determine statistics of de novo assembly graphs</description>
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="version_command"/>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 @HEADLESS@
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12 Bandage
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13 info
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14 '$input_file'
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15 $tsv
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16 | sed 's/:\s\+/:\t/g'
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17 > out.tab
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18 ]]></command>
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19 <inputs>
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20 <param name="input_file" type="data" format="txt" label="Graphical Fragment Assembly" help="Supports multiple assembly graph formats: LastGraph (Velvet), FASTG (SPAdes), Trinity.fasta, ASQG and GFA."/>
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21 <param argument="--tsv" type="boolean" checked="false" truevalue="--tsv" falsevalue="" label="Output the information in a single tab-delimited line starting with the graph file"/>
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22 </inputs>
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23 <outputs>
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24 <data name="outfile" format="tabular" from_work_dir="out.tab" label="${tool.name} on ${on_string}: Assembly Graph Information"/>
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="input_file" ftype="tabular" value="gfa.tabular"/>
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29 <param name="select_mode" value="info"/>
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30 <param name="tsv" value="True"/>
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31 <output name="outfile" ftype="tabular" file="out.tab" compare="contains"/>
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32 </test>
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33 <test>
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34 <param name="input_file" ftype="tabular" value="gfa.tabular"/>
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35 <param name="select_mode" value="info"/>
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36 <output name="outfile" ftype="tabular" file="out_standard.tab"/>
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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41 @BANDAGE_OVERVIEW@
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43 **Command Documentation**
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44
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45 ``Bandage info`` takes a graph file as input and outputs the following statistics about the graph:
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46
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47 - **Node count:** The number of nodes in the graph. Only positive nodes are counted (i.e. each complementary pair counts as one).
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48 - **Edge count:** The number of edges in the graph. Only one edge in each complementary pair is counted.
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49 - **Total length:** The total number of base pairs in the graph.
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50 - **Dead ends:** The number of instances where an end of a node does not connect to any other nodes.
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51 - **Percentage dead ends:** The proportion of possible dead ends. The maximum number of dead ends is twice the number of nodes (occurs when there are no edges), so this value is the number of dead ends divided by twice the node count.
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52 - **Connected components:** The number of regions of the graph which are disconnected from each other.
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53 - **Largest component:** The total number of base pairs in the largest connected component.
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54 - **N50:** Nodes that are this length or greater will collectively add up to at least half of the total length.
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55 - **Shortest node:** The length of the shortest node in the graph.
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56 - **Lower quartile node:** The median node length for the shorter half of the nodes.
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57 - **Median node:** The median node length for the graph.
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58 - **Upper quartile node:** The median node length for the longer half of the nodes.
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59 - **Longest node:** The length of the longest node in the graph.
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60
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61 Example output::
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62
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63 Node count: 561
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64 Edge count: 734
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65 Total length (bp): 4878380
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66 Dead ends: 33
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67 Percentage dead ends: 2.94118%
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68 Connected components: 19
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69 Largest component (bp): 4821329
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70 N50 (bp): 90360
0
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71 Shortest node (bp): 1
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72 Lower quartile node (bp): 17
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73 Median node (bp): 87
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74 Upper quartile node (bp): 404
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75 Longest node (bp): 205425
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76
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77 ]]></help>
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78 <expand macro="citations"/>
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79 </tool>