Mercurial > repos > jvolkening > b2b_summarize_assembly

annotate summarize_assembly.xml @ 1:cd86d5f93b4a draft default tip

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
author jvolkening
date Fri, 08 Mar 2024 00:45:00 +0000
parents 1995630ef409
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1 <tool id="b2b_summarize_assembly" name="Summarize assembly"
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2 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT" profile="21.01">
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4 <description>Calculate and print basic assembly summary stats</description>
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5 <macros>
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6 <token name="@TOOL_NAME@">summarize_assembly</token>
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7 <token name="@TOOL_VERSION@">0.02</token>
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8 <token name="@VERSION_SUFFIX@">1</token>
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9 <import>macros.xml</import>
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10 </macros>
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11 <edam_topics>
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12 <edam_topic>topic_0080</edam_topic> <!-- Sequence analysis -->
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13 </edam_topics>
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14 <expand macro="requirements" />
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15 <expand macro="version_command" />
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17 <!-- ***************************************************************** -->
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19 <command detect_errors="aggressive">
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20 <![CDATA[
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22 summarize_assembly
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23 --fasta $input1
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24 --cutoffs $cutoffs
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25 #if $split_N:
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26 --split_N
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27 #end if
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28 #if $strip_N:
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29 --strip_N
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30 #end if
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32 > $report
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33 ;
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35 ]]>
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36 </command>
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38 <!-- ***************************************************************** -->
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40 <inputs>
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41 <param format="fasta" name="input1" type="data" label="Assembly in FASTA format" />
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42 <param name="cutoffs" type="text" size="60" value="50 90" label="Nx cutoffs to calculate (space-separated)">
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43 <sanitizer invalid_char="">
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44 <valid initial="string.digits"><add value=" " /></valid>
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45 </sanitizer>
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46 </param>
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47 <param name="strip_N" type="boolean" label="Strip Ns prior to calculations" />
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48 <param name="split_N" type="boolean" label="Split scaffolds on Ns (e.g. report contig-level summary)" />
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49 </inputs>
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50
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51 <!-- ***************************************************************** -->
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52
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53 <outputs>
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54 <data format="txt" name="report" label="${tool.name} on ${on_string}" />
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55 </outputs>
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57 <!-- ***************************************************************** -->
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59 <tests>
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60 <test>
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61 <param name="input1" value="assembly.fa" ftype="fasta" />
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62 <param name="cutoffs" value="50 90 95" />
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63 <output name="report" file="summarize.txt" compare="diff" />
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64 </test>
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65 <test>
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66 <param name="input1" value="assembly.fa" ftype="fasta" />
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67 <param name="cutoffs" value="50 90 95" />
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68 <param name="strip_N" value="True" />
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69 <output name="report" file="summarize.strip.txt" compare="diff" />
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70 </test>
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71 <test>
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72 <param name="input1" value="assembly.fa" ftype="fasta" />
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73 <param name="cutoffs" value="50 90 95" />
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74 <param name="split_N" value="True" />
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75 <output name="report" file="summarize.split.txt" compare="diff" />
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76 </test>
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77 </tests>
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79 <!-- ***************************************************************** -->
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81 <help>
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82
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83 summarize_assembly is a utility from b2b-utils. It takes a FASTA file and
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84 optionally a list of cutoff values as input and prints out summary
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85 information about the contigs/scaffolds contained in the file. You can, of
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86 course, supply a FASTA file of any sort of nucleic acid sequences, but the
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87 summary information makes most sense for contigs from genomic sequencing
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88 assemblies.
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89
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90 </help>
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91
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92 <!-- ***************************************************************** -->
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93
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94 <citations>
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95 </citations>
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96
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97 </tool>
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98