Mercurial > repos > jvolkening > b2b_summarize_assembly

annotate summarize_assembly.xml @ 0:1995630ef409 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
author jvolkening
date Sat, 02 Mar 2024 07:44:53 +0000
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1 <tool id="b2b_summarize_assembly" name="Summarize assembly" version="0.02">
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3 <description>Calculate and print basic assembly summary stats</description>
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5 <!-- ***************************************************************** -->
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7 <requirements>
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8 <requirement type="package" version="0.019">b2b-utils</requirement>
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9 </requirements>
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11 <!-- ***************************************************************** -->
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13 <version_command>summarize_assembly --version | perl -wnE'print "$1\n" for /summarize_assembly v(.+)/g'</version_command>
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15 <!-- ***************************************************************** -->
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17 <command detect_errors="aggressive">
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18 <![CDATA[
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20 summarize_assembly
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21 --fasta $input1
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22 --cutoffs $cutoffs
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23 #if $split_N:
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24 --split_N
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25 #end if
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26 #if $strip_N:
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27 --strip_N
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28 #end if
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30 > $report
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31 ;
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33 ]]>
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34 </command>
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36 <!-- ***************************************************************** -->
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38 <inputs>
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39 <param format="fasta" name="input1" type="data" label="Assembly in FASTA format" />
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40 <param name="cutoffs" type="text" size="60" value="50 90" label="Nx cutoffs to calculate (space-separated)">
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41 <sanitizer invalid_char="">
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42 <valid initial="string.digits"><add value=" " /></valid>
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43 </sanitizer>
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44 </param>
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45 <param name="strip_N" type="boolean" label="Strip Ns prior to calculations" />
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46 <param name="split_N" type="boolean" label="Split scaffolds on Ns (e.g. report contig-level summary)" />
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47 </inputs>
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48
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49 <!-- ***************************************************************** -->
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51 <outputs>
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52 <data format="txt" name="report" label="${tool.name} on ${on_string}" />
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53 </outputs>
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54
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55 <!-- ***************************************************************** -->
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57 <tests>
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58 <test>
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59 <param name="input1" value="assembly.fa" ftype="fasta" />
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60 <param name="cutoffs" value="50 90 95" />
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61 <output name="report" file="summarize.txt" compare="diff" />
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62 </test>
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63 <test>
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64 <param name="input1" value="assembly.fa" ftype="fasta" />
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65 <param name="cutoffs" value="50 90 95" />
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66 <param name="strip_N" value="True" />
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67 <output name="report" file="summarize.strip.txt" compare="diff" />
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68 </test>
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69 <test>
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70 <param name="input1" value="assembly.fa" ftype="fasta" />
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71 <param name="cutoffs" value="50 90 95" />
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72 <param name="split_N" value="True" />
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73 <output name="report" file="summarize.split.txt" compare="diff" />
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74 </test>
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75 </tests>
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76
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77 <!-- ***************************************************************** -->
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79 <help>
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81 summarize_assembly is a utility from b2b-utils. It takes a FASTA file and
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82 optionally a list of cutoff values as input and prints out summary
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83 information about the contigs/scaffolds contained in the file. You can, of
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84 course, supply a FASTA file of any sort of nucleic acid sequences, but the
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85 summary information makes most sense for contigs from genomic sequencing
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86 assemblies.
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87
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88 </help>
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90 <!-- ***************************************************************** -->
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92 <citations>
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93 </citations>
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95 </tool>
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