Mercurial > repos > jdv > b2b_summarize_assembly

annotate summarize_assembly.xml @ 1:5def63878840 draft default tip

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"planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
author jdv
date Tue, 28 Sep 2021 06:16:07 +0000
parents 114353d77370
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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 <!--
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9 <requirement type="package" version="0.003">b2b-utils</requirement>
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10 -->
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11 <requirement type="package" version="0.008002">perl-biox-seq</requirement>
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12 <requirement type="package">perl-list-moreutils</requirement>
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13 </requirements>
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15 <!-- ***************************************************************** -->
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17 <version_command>perl $__tool_directory__/summarize_assembly --version | perl -wnE'print "$1\n" for /summarize_assembly v(.+)/g'</version_command>
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19 <!-- ***************************************************************** -->
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21 <command detect_errors="aggressive">
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22 <![CDATA[
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23
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24 perl $__tool_directory__/summarize_assembly
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25 --fasta $input1
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26 --cutoffs $cutoffs
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27 #if $split_N:
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28 --split_N
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29 #end if
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30 #if $strip_N:
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31 --strip_N
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32 #end if
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34 > $report
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35 ;
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37 ]]>
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38 </command>
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40 <!-- ***************************************************************** -->
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42 <inputs>
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43 <param format="fasta" name="input1" type="data" label="Assembly in FASTA format" />
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44 <param name="cutoffs" type="text" size="60" value="50 90" label="Nx cutoffs to calculate (space-separated)">
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45 <sanitizer invalid_char="">
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46 <valid initial="string.digits"><add value=" " /></valid>
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47 </sanitizer>
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48 </param>
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49 <param name="strip_N" type="boolean" label="Strip Ns prior to calculations" />
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50 <param name="split_N" type="boolean" label="Split scaffolds on Ns (e.g. report contig-level summary)" />
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51 </inputs>
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52
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53 <!-- ***************************************************************** -->
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55 <outputs>
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56 <data format="txt" name="report" label="${tool.name} on ${on_string}" />
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57 </outputs>
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59 <!-- ***************************************************************** -->
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61 <tests>
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62 <test>
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63 <param name="input1" value="assembly.fa" ftype="fasta" />
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64 <param name="cutoffs" value="50 90 95" />
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65 <output name="report" file="summarize.txt" compare="diff" />
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66 </test>
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67 <test>
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68 <param name="input1" value="assembly.fa" ftype="fasta" />
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69 <param name="cutoffs" value="50 90 95" />
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70 <param name="strip_N" value="True" />
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71 <output name="report" file="summarize.strip.txt" compare="diff" />
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72 </test>
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73 <test>
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74 <param name="input1" value="assembly.fa" ftype="fasta" />
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75 <param name="cutoffs" value="50 90 95" />
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76 <param name="split_N" value="True" />
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77 <output name="report" file="summarize.split.txt" compare="diff" />
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78 </test>
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79 </tests>
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80
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81 <!-- ***************************************************************** -->
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83 <help>
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84
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85 summarize_assembly is a utility from b2b-utils. It takes a FASTA file and
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86 optionally a list of cutoff values as input and prints out summary
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87 information about the contigs/scaffolds contained in the file. You can, of
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88 course, supply a FASTA file of any sort of nucleic acid sequences, but the
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89 summary information makes most sense for contigs from genomic sequencing
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90 assemblies.
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91
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92 </help>
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94 <!-- ***************************************************************** -->
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95
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96 <citations>
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97 </citations>
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98
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99 </tool>
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100