Mercurial > repos > iuc > nanopolishcomp_freqmethcalculate

annotate freqmethcalculate.xml @ 1:f08dfdcefdbd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp commit fc685e81241eb196e57669961a42d03c60e7c9b6
author iuc
date Wed, 13 Mar 2024 11:52:05 +0000
parents 80b6e23cb70d
children
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1 <?xml version="1.0"?>
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2 <tool id="nanopolishcomp_freqmethcalculate" name="NanopolishComp: FreqMethCalculate" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
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3 <description>calculates methylation frequency at genomic CpG sites</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
1
f08dfdcefdbd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp commit fc685e81241eb196e57669961a42d03c60e7c9b6
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7 <expand macro="xrefs"/>
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8 <expand macro="requirements"/>
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9 <expand macro="version_command"/>
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10 <command detect_errors="exit_code"><![CDATA[
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11 NanopolishComp Freq_meth_calculate
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12 ## required
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13 -i '$i'
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14 ## optional
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15 -d $d
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16 #if $f
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17 -f '$f'
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18 #end if
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19 #if $s
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20 -s '$s'
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21 #end if
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22 $strand_specific
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23 --min_llr $min_llr
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24 -b 'result.bed'
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25 -t 'result.tsv'
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26 -v
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27 ]]></command>
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28 <inputs>
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29 <param argument="-i" type="data" format="tabular" label="Select nanopolish call methylation file"/>
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30 <param argument="-d" type="integer" value="10" min="0" label="Set minimal number of reads covering a site to be reported"/>
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31 <param argument="-f" type="data" format="fai" optional="true" label="Select fasta index file" help="Obtained with samtools faidx. Required for coordinate sorting"/>
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32 <param argument="-s" type="text" value="" optional="true" label="Set sample ID" help="Used for bed track header."/>
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33 <param argument="--strand_specific" type="boolean" truevalue="--strand_specific" falsevalue="" label="Are sites strand specific?"/>
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34 <param argument="--min_llr" type="integer" value="2" min="0" label="Set minimal log likelyhood ratio" help="To consider a site significantly methylated or unmethylated."/>
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35 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
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36 <option value="bed" selected="true">Methylation frequency (BED)</option>
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37 <option value="tsv" selected="true">Methylation frequency (Tabular)</option>
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38 </param>
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39 </inputs>
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40 <outputs>
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41 <data name="out_bed" format="bed" from_work_dir="result.bed" label="${tool.name} on ${on_string}: Methylation frequency (BED)">
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42 <filter>'bed' in out</filter>
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43 </data>
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44 <data name="out_tsv" format="tabular" from_work_dir="result.tsv" label="${tool.name} on ${on_string}: Methylation frequency (Tabular)">
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45 <filter>'tsv' in out</filter>
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46 </data>
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47 </outputs>
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48 <tests>
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49 <!-- #1 default -->
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50 <test expect_num_outputs="2">
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51 <param name="i" value="sample_meth.tsv"/>
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52 <output name="out_bed">
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53 <assert_contents>
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54 <has_n_lines n="56"/>
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55 <has_line line="track name=Methylation_ itemRgb=On"/>
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56 <has_text_matching expression="tig00000001&#009;201961.+"/>
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57 </assert_contents>
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58 </output>
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59 <output name="out_tsv">
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60 <assert_contents>
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61 <has_n_lines n="56"/>
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62 <has_text_matching expression="chromosome&#009;start.+"/>
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63 <has_text_matching expression="tig00000001&#009;201961.+"/>
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64 </assert_contents>
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65 </output>
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66 </test>
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67 <!-- #2 -->
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68 <test expect_num_outputs="2">
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69 <param name="i" value="sample_meth.tsv"/>
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70 <param name="d" value="11"/>
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71 <param name="s" value="test"/>
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72 <param name="strand_specific" value="true"/>
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73 <param name="min_llr" value="3"/>
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74 <param name="out" value="bed,tsv"/>
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75 <output name="out_bed">
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76 <assert_contents>
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77 <has_n_lines n="111"/>
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78 <has_line line="track name=Methylation_test itemRgb=On"/>
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79 <has_text_matching expression="tig00000001&#009;200009.+"/>
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80 </assert_contents>
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81 </output>
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82 <output name="out_tsv">
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83 <assert_contents>
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84 <has_n_lines n="111"/>
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85 <has_text_matching expression="chromosome&#009;start.+"/>
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86 <has_text_matching expression="tig00000001&#009;201961.+"/>
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87 </assert_contents>
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88 </output>
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89 </test>
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90 </tests>
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91 <help><![CDATA[
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92 .. class:: infomark
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93
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94 **What it does**
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95
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96 @WID@
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97
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98 Freq_meth_calculate calculates methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.
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99
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100 **Input**
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101
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102 A nanopolish call methylation tabular output file.
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103
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104 **Output**
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105
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106 *BED file*
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107
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108 Standard genomic BED6. The score correspond to the methylation frequency multiplied by 1000. The file is sorted by coordinates and can be rendered with a genome browser such as IGV
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109
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110 *Tabulated TSV file*
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111
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112 Contrary to the bed file, in the tabulated report, positions are ordered by decreasing methylation frequency.
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113
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114 The file contains the following fields:
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115
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116 - chrom / start / end / strand: Genomic coordinates of the motif or group of motifs in case split_group was not selected.
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117 - site_id: Unique integer identifier of the genomic position.
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118 - methylated_reads / unmethylated_reads / ambiguous_reads: Number of reads at a given genomic location with a higher likelyhood of being methylated or unmethylated or with an ambiguous methylation call.
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119 - sequence: -5 to +5 sequence of the motif or group of motifs in case split_group was not selected.
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120 - num_motifs: Number of motif in the group.
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121 - meth_freq: Methylation frequency (out of non anbiguous calls).
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122
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123 .. class:: infomark
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124
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125 **References**
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126
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127 @REFERENCES@
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128 ]]></help>
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129 <expand macro="citations"/>
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130 </tool>