Mercurial > repos > iuc > windowmasker

annotate windowmasker_mkcounts.xml @ 0:d90ae4a02efd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
author iuc
date Thu, 14 Dec 2023 16:04:27 +0000
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0
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
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1 <tool id="windowmasker_mkcounts" name="WindowMasker mkcounts" version="1.0" profile="22.01">
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2 <description>Construct WindowMasker unit counts table</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 windowmasker -mk_counts -infmt fasta
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10 #if $adv.genome_size
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11 -genome_size $adv.genome_size
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12 #end if
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13 #if $adv.t_low
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14 -t_low $adv.t_low
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15 #end if
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16 #if $adv.t_high
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17 -t_high $adv.t_high
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18 #end if
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19 #if $adv.unit
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20 -unit $adv.unit
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21 #end if
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22
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23 -sformat ${adv.sformat}
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24 ${adv.checkdup}
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25 -in '${fasta_input}'
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26 -out '${mkcount_output}'
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27 ]]>
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28 </command>
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29 <inputs>
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30 <param argument="-in" name="fasta_input" type="data" format="fasta"
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31 label="FASTA sequence file" />
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32
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33 <section name="adv" title="Advanced options" expanded="false" >
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34 <param argument="-checkdup" type="boolean" checked="false"
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35 truevalue="-checkdup" falsevalue=""
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36 label="Check input file for potentially duplicated sequences" />
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37
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38 <param argument="-genome_size" type="integer" label="Genome size"
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39 min="0" optional="true"
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40 help="Use this genome size to compute the unit length" />
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41
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42 <param argument="-sformat" type="select" label="Unit counts format"
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43 help="The format the unit counts data should be generated" >
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44 <option value="ascii">Plain text (ascii)</option>
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45 <option value="oascii" selected="true">Optimized text (oascii)</option>
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46 <!-- Omit support for non-portable binary formats (binary, obinary) -->
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47 </param>
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48
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49 <param argument="-t_low" type="integer" label="T_low"
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50 min="0" optional="true"
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51 help="Save only units that appears at least this many times" />
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52
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53 <param argument="-t_high" type="integer" label="T_high"
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54 min="0" optional="true"
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55 help="Set the maximum count value for units" />
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56
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57 <param argument="-unit" type="integer" label="Unit length"
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58 min="1" max="16" optional="true"
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59 help="Unit length used to mask the genome" />
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60 </section>
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61 </inputs>
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62 <outputs>
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63 <data name="mkcount_output" format="txt" />
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64 </outputs>
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65 <tests>
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66 <test>
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67 <!-- Test mkcounts with default settings -->
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68 <param name="fasta_input" value="chr4_part.fa" ftype="fasta" />
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69 <output name="mkcount_output" file="chr4_part.oascii.counts" />
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70 </test>
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71 <test>
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72 <!-- Test mkcounts with custom genome_size -->
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73 <param name="fasta_input" value="chr4_part.fa" ftype="fasta" />
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74 <param name="genome_size" value="500000" />
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75 <output name="mkcount_output" file="chr4_part.500k_size.counts" />
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76 </test>
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77 <test>
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78 <!-- Test mkcounts with ascii output format -->
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79 <param name="fasta_input" value="chr4_part.fa" ftype="fasta" />
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80 <param name="sformat" value="ascii" />
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81 <output name="mkcount_output" file="chr4_part.ascii.counts" />
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82 </test>
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83 <test>
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84 <!-- Test mkcounts with custom unit settings -->
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85 <param name="fasta_input" value="chr4_part.fa" ftype="fasta" />
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86 <param name="t_low" value="3" />
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87 <param name="t_high" value="20" />
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88 <param name="unit" value="9" />
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89 <output name="mkcount_output" file="chr4_part.custom_unit.counts" />
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90 </test>
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91 </tests>
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92 <help>
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93 <![CDATA[
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94 **What it does**
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95
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96 This tool runs `stage 1 <https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/>`_
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97 of the WindowMasker analysis to produce a unit counts file for a genome assembly.
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98
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99 ]]></help>
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100 <expand macro="citations" />
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101 </tool>