Mercurial > repos > iuc > nanopolishcomp_freqmethcalculate

annotate freqmethcalculate.xml @ 0:80b6e23cb70d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
author iuc
date Tue, 12 May 2020 17:08:21 -0400
parents
children f08dfdcefdbd
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0
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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>
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7 <expand macro="requirements"/>
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8 <expand macro="version_command"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 NanopolishComp Freq_meth_calculate
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11 ## required
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12 -i '$i'
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13 ## optional
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14 -d $d
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15 #if $f
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16 -f '$f'
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17 #end if
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18 #if $s
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19 -s '$s'
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20 #end if
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21 $strand_specific
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22 --min_llr $min_llr
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23 -b 'result.bed'
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24 -t 'result.tsv'
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25 -v
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26 ]]></command>
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27 <inputs>
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28 <param argument="-i" type="data" format="tabular" label="Select nanopolish call methylation file"/>
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29 <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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30 <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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31 <param argument="-s" type="text" value="" optional="true" label="Set sample ID" help="Used for bed track header."/>
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32 <param argument="--strand_specific" type="boolean" truevalue="--strand_specific" falsevalue="" label="Are sites strand specific?"/>
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33 <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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34 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
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35 <option value="bed" selected="true">Methylation frequency (BED)</option>
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36 <option value="tsv" selected="true">Methylation frequency (Tabular)</option>
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37 </param>
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38 </inputs>
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39 <outputs>
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40 <data name="out_bed" format="bed" from_work_dir="result.bed" label="${tool.name} on ${on_string}: Methylation frequency (BED)">
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41 <filter>'bed' in out</filter>
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42 </data>
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43 <data name="out_tsv" format="tabular" from_work_dir="result.tsv" label="${tool.name} on ${on_string}: Methylation frequency (Tabular)">
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44 <filter>'tsv' in out</filter>
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45 </data>
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46 </outputs>
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47 <tests>
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48 <!-- #1 default -->
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49 <test expect_num_outputs="2">
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50 <param name="i" value="sample_meth.tsv"/>
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51 <output name="out_bed">
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52 <assert_contents>
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53 <has_n_lines n="56"/>
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54 <has_line line="track name=Methylation_ itemRgb=On"/>
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55 <has_text_matching expression="tig00000001&#009;201961.+"/>
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56 </assert_contents>
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57 </output>
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58 <output name="out_tsv">
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59 <assert_contents>
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60 <has_n_lines n="56"/>
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61 <has_text_matching expression="chromosome&#009;start.+"/>
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62 <has_text_matching expression="tig00000001&#009;201961.+"/>
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63 </assert_contents>
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64 </output>
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65 </test>
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66 <!-- #2 -->
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67 <test expect_num_outputs="2">
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68 <param name="i" value="sample_meth.tsv"/>
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69 <param name="d" value="11"/>
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70 <param name="s" value="test"/>
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71 <param name="strand_specific" value="true"/>
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72 <param name="min_llr" value="3"/>
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73 <param name="out" value="bed,tsv"/>
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74 <output name="out_bed">
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75 <assert_contents>
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76 <has_n_lines n="111"/>
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77 <has_line line="track name=Methylation_test itemRgb=On"/>
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78 <has_text_matching expression="tig00000001&#009;200009.+"/>
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79 </assert_contents>
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80 </output>
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81 <output name="out_tsv">
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82 <assert_contents>
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83 <has_n_lines n="111"/>
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84 <has_text_matching expression="chromosome&#009;start.+"/>
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85 <has_text_matching expression="tig00000001&#009;201961.+"/>
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86 </assert_contents>
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87 </output>
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88 </test>
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89 </tests>
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90 <help><![CDATA[
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91 .. class:: infomark
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92
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93 **What it does**
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94
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95 @WID@
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96
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97 Freq_meth_calculate calculates methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.
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98
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99 **Input**
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100
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101 A nanopolish call methylation tabular output file.
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102
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103 **Output**
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104
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105 *BED file*
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106
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107 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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108
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109 *Tabulated TSV file*
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110
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111 Contrary to the bed file, in the tabulated report, positions are ordered by decreasing methylation frequency.
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112
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113 The file contains the following fields:
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114
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115 - chrom / start / end / strand: Genomic coordinates of the motif or group of motifs in case split_group was not selected.
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116 - site_id: Unique integer identifier of the genomic position.
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117 - 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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118 - sequence: -5 to +5 sequence of the motif or group of motifs in case split_group was not selected.
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119 - num_motifs: Number of motif in the group.
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120 - meth_freq: Methylation frequency (out of non anbiguous calls).
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121
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122 .. class:: infomark
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123
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124 **References**
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125
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126 @REFERENCES@
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127 ]]></help>
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128 <expand macro="citations"/>
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129 </tool>