Mercurial > repos > yating-l > windowmasker_2_5_0
annotate windowmasker_mkcounts.xml @ 0:f80c9e6700ba draft default tip
planemo upload commit 91a780909d1eda07d17f6aebf7f08f0c024b6a25
author | yating-l |
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date | Tue, 16 May 2017 13:18:12 -0400 |
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1 <?xml version="1.0"?> |
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2 <tool id="windowmasker_mkcounts" name="WindowMasker_mkcounts" version="1.0"> |
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3 <description>Construct WindowMasker unit counts table</description> |
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4 |
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5 <macros> |
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6 <import>windowmasker_macros.xml</import> |
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7 </macros> |
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8 |
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9 <expand macro="requirements" /> |
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10 |
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11 <command detect_errors="exit_code"> |
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12 <![CDATA[ |
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13 @OPTIONAL_PARAM_FUNC@ |
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14 |
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15 windowmasker -mk_counts -infmt fasta |
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16 |
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17 $optional_param("-genome_size", $adv.genome_size) |
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18 $optional_param("-t_low", $adv.t_low) |
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19 $optional_param("-t_high", $adv.t_high) |
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20 $optional_param("-unit", $adv.unit) |
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21 |
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22 -sformat ${adv.sformat} -checkdup ${adv.checkdup} |
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23 -in "${fasta_input}" -out "${mkcount_output}" |
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24 ]]> |
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25 </command> |
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26 <inputs> |
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27 <param name="fasta_input" type="data" format="fasta" |
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28 label="FASTA sequence file" /> |
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29 |
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30 <section name="adv" title="Advanced options" expanded="false" > |
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31 <param name="checkdup" type="boolean" checked="false" |
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32 truevalue="true" falsevalue="false" |
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33 label="Check input file for potentially duplicated sequences" |
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34 help="-checkdup" /> |
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35 |
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36 <param name="genome_size" type="integer" label="Genome size" |
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37 min="0" optional="true" |
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38 help="Use this genome size to compute the unit length" /> |
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39 |
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40 <param name="sformat" type="select" label="Unit counts format" |
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41 help="The format the unit counts data should be generated" > |
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42 |
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43 <option value="ascii">Plain text (ascii)</option> |
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44 <option value="oascii" selected="true">Optimized text (oascii)</option> |
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45 <!-- Omit support for non-portable binary formats (binary, obinary) --> |
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46 </param> |
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47 |
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48 <param name="t_low" type="integer" label="T_low" |
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49 min="0" optional="true" |
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50 help="Save only units that appears at least this many times" /> |
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51 |
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52 <param name="t_high" type="integer" label="T_high" |
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53 min="0" optional="true" |
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54 help="Set the maximum count value for units" /> |
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55 |
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56 <param name="unit" type="integer" label="Unit length" |
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57 min="1" max="16" optional="true" |
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58 help="Unit length used to mask the genome" /> |
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59 </section> |
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60 </inputs> |
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61 <outputs> |
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62 <data name="mkcount_output" format="txt" /> |
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63 </outputs> |
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64 <tests> |
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65 <test> |
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66 <!-- Test mkcounts with default settings --> |
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67 <param name="fasta_input" value="chr4_part.fa" ftype="fasta" /> |
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68 <output name="mkcount_output" file="chr4_part.oascii.counts" /> |
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69 </test> |
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70 <test> |
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71 <!-- Test mkcounts with custom genome_size --> |
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72 <param name="fasta_input" value="chr4_part.fa" ftype="fasta" /> |
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73 <param name="genome_size" value="500000" /> |
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74 <output name="mkcount_output" file="chr4_part.500k_size.counts" /> |
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75 </test> |
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76 <test> |
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77 <!-- Test mkcounts with ascii output format --> |
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78 <param name="fasta_input" value="chr4_part.fa" ftype="fasta" /> |
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79 <param name="sformat" value="ascii" /> |
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80 <output name="mkcount_output" file="chr4_part.ascii.counts" /> |
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81 </test> |
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82 <test> |
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83 <!-- Test mkcounts with custom unit settings --> |
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84 <param name="fasta_input" value="chr4_part.fa" ftype="fasta" /> |
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85 <param name="t_low" value="3" /> |
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86 <param name="t_high" value="20" /> |
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87 <param name="unit" value="9" /> |
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88 <output name="mkcount_output" file="chr4_part.custom_unit.counts" /> |
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89 </test> |
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90 </tests> |
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91 <help> |
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92 <![CDATA[ |
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93 **What it does** |
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94 |
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95 This tool runs `stage 1 <https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/>`_ |
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96 of the WindowMasker analysis to produce a unit counts file for a genome assembly. |
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97 |
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98 ]]></help> |
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99 |
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100 <expand macro="citations" /> |
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101 </tool> |