Mercurial > repos > jdv > b2b_summarize_assembly

annotate summarize_assembly.xml @ 0:114353d77370 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
author jdv
date Wed, 17 Jul 2019 17:49:39 -0400
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114353d77370 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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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="0.006007">perl-biox-seq</requirement>
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12 </requirements>
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14 <!-- ***************************************************************** -->
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16 <version_command>summarize_assembly --version | perl -wnE'print "$1\n" for /summarize_assembly v(.+)/g'</version_command>
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18 <!-- ***************************************************************** -->
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20 <command detect_errors="aggressive">
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21 <![CDATA[
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23 summarize_assembly
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24 --fasta $input1
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25 --cutoffs $cutoffs
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26 #if $split_N:
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27 --split_N
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28 #end if
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29 #if $strip_N:
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30 --strip_N
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31 #end if
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33 > $report
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34 ;
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36 ]]>
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37 </command>
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39 <!-- ***************************************************************** -->
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41 <inputs>
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42 <param format="fasta" name="input1" type="data" label="Assembly in FASTA format" />
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43 <param name="cutoffs" type="text" size="60" value="50 90" label="Nx cutoffs to calculate (space-separated)">
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44 <sanitizer invalid_char="">
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45 <valid initial="string.digits"><add value=" " /></valid>
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46 </sanitizer>
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47 </param>
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48 <param name="strip_N" type="boolean" label="Strip Ns prior to calculations" />
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49 <param name="split_N" type="boolean" label="Split scaffolds on Ns (e.g. report contig-level summary)" />
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50 </inputs>
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51
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52 <!-- ***************************************************************** -->
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54 <outputs>
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55 <data format="txt" name="report" label="${tool.name} on ${on_string}" />
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56 </outputs>
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57
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58 <!-- ***************************************************************** -->
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59
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60 <tests>
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61 <test>
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62 <param name="input1" value="assembly.fa" ftype="fasta" />
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63 <param name="cutoffs" value="50 90 95" />
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64 <output name="report" file="summarize.txt" compare="diff" />
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65 </test>
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66 <test>
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67 <param name="input1" value="assembly.fa" ftype="fasta" />
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68 <param name="cutoffs" value="50 90 95" />
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69 <param name="strip_N" value="True" />
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70 <output name="report" file="summarize.strip.txt" compare="diff" />
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71 </test>
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72 <test>
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73 <param name="input1" value="assembly.fa" ftype="fasta" />
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74 <param name="cutoffs" value="50 90 95" />
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75 <param name="split_N" value="True" />
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76 <output name="report" file="summarize.split.txt" compare="diff" />
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77 </test>
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78 </tests>
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79
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80 <!-- ***************************************************************** -->
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82 <help>
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83
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84 summarize_assembly is a utility from b2b-utils. It takes a FASTA file and
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85 optionally a list of cutoff values as input and prints out summary
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86 information about the contigs/scaffolds contained in the file. You can, of
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87 course, supply a FASTA file of any sort of nucleic acid sequences, but the
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88 summary information makes most sense for contigs from genomic sequencing
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89 assemblies.
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90
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91 </help>
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93 <!-- ***************************************************************** -->
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95 <citations>
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96 </citations>
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98 </tool>
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