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annotate tetyper.xml @ 24:ea14ef930fc5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 3803eff127b827b669627f7a529e84142812fc56-dirty"
author dfornika
date Fri, 10 Jan 2020 18:52:22 +0000
parents 7158a1df3841
children 98d8bd5e9058
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1 <tool id="tetyper" name="TETyper" version="@TOOL_VERSION@+galaxy1">
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2 <description>Transposable Element Typer</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.1</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">tetyper</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 TETyper.py
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12 --threads \${GALAXY_SLOTS:-1}
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13 #if $collection_paired.selector == "paired"
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14 --fq1 '${collection_paired.forward_input}' --fq2 '${collection_paired.reverse_input}'
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15 #elif $collection_paired.selector == "collection":
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16 --fq1 '${collection_paired.input_pair.forward}' --fq2 '${collection_paired.input_pair.reverse}'
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17 #end if
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18 --ref '${reference}'
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19 --flank_len '${flank_length}'
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20 --min_reads '${min_reads}'
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21 --min_each_strand '${min_each_strand}'
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22 --min_mapped_len '${min_mapped_len}'
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23 --min_qual '${min_qual}'
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24 #if str( $snp_profiles_source.snp_profiles_source_selector ) == "tool_data_table":
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25 #set $snp_profiles = str( $snp_profiles_source.snp_profiles.fields.path )
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26 #else:
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27 #set $snp_profiles = str( $snp_profiles_source.snp_profiles )
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28 #end if
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29 #if str( $snp_profiles ) != 'None'
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30 --snp_profiles '${snp_profiles}'
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31 #end if
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32 #if str( $struct_profiles_source.struct_profiles_source_selector ) == "tool_data_table":
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33 #set $struct_profiles = str( $struct_profiles_source.struct_profiles.fields.path )
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34 #else:
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35 #set $struct_profiles = str( $struct_profiles_source.struct_profiles )
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36 #end if
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37 #if str( $struct_profiles ) != 'None'
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38 --struct_profiles '${struct_profiles}'
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39 #end if
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40 --outprefix output
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41 ]]>
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42 </command>
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43 <inputs>
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44 <conditional name="collection_paired">
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45 <param name="selector" type="select" label="Collection or paired reads" >
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46 <option value="collection">Collection</option>
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47 <option value="paired" selected="True">Paired</option>
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48 </param>
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49 <when value="collection">
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50 <param format="fastq,fastq.gz" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" />
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51 </when>
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52 <when value="paired">
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53 <param format="fastq,fastq.gz" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>
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54 <param format="fastq,fastq.gz" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>
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55 </when>
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56 </conditional>
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57 <conditional name="snp_profiles_source">
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58 <param name="snp_profiles_source_selector" type="select" label="Select a SNP profile from your history or use one from a tool data table?">
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59 <option value="tool_data_table">From tool data table</option>
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60 <option value="history" selected="true">From history</option>
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61 </param>
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62 <when value="tool_data_table">
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63 <param name="snp_profiles" type="select" format="tabular" optional="true">
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64 <options from_data_table="tetyper_snp_profiles">
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65 <validator type="no_options" message="No TETyper SNP profiles are available" />
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66 </options>
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67 </param>
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68 </when>
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69 <when value="history">
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70 <param name="snp_profiles" type="data" format="tabular" label="SNP Profile" help="A three-column tabular file with SNP profile definitions" optional="true"/>
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71 </when>
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72 </conditional>
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73 <conditional name="struct_profiles_source">
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74 <param name="struct_profiles_source_selector" type="select" label="Select a structural variant profile from your history or use one from a tool data table?">
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75 <option value="tool_data_table">From tool data table</option>
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76 <option value="history" selected="true">From history</option>
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77 </param>
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78 <when value="tool_data_table">
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79 <param name="struct_profiles" type="select" format="tabular" optional="true">
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80 <options from_data_table="tetyper_struct_profiles">
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81 <validator type="no_options" message="No TETyper structural variant profiles are available" />
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82 </options>
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83 </param>
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84 </when>
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85 <when value="history">
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86 <param name="struct_profiles" type="data" format="tabular" label="Structural Variant Profile" help="A two-column tabular file with structural variant profile definitions" optional="true"/>
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87 </when>
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88 </conditional>
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89 <param name="reference" type="data" format="fasta" label="Transposable Element Reference"/>
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90 <param name="flank_length" type="integer" min="4" value="5" max="16" label="Flank Length" help="Length of flanking region to extract."/>
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91 <param name="min_reads" type="integer" min="1" value="10" max="100" label="Minimum Reads" help="Minimum read number for including a specific flanking sequence."/>
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92 <param name="min_each_strand" type="integer" min="1" value="1" max="100" label="Minimum Reads (each strand)" help="Minimum read number for each strand for including a specific flanking sequence."/>
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93 <param name="min_mapped_len" type="integer" min="8" value="30" max="100" label="Minimum Mapped Length" help="Minimum length of mapping for a read to be used in determining flanking sequences. Higher values are more robust to spurious mapping. Lower values will recover more reads."/>
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94 <param name="min_qual" type="integer" min="0" value="10" max="100" label="Minimum quality" help="Minimum quality value across extracted flanking sequence." />
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95 <param name="include_log" type="boolean" label="Include log in output"/>
0
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96 </inputs>
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97 <outputs>
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98 <data name="summary" format="tabular" from_work_dir="output_summary.txt" label="${tool.name} on ${on_string}: summary"/>
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99 <data name="snps" format="vcf" from_work_dir="output.vcf" label="${tool.name} on ${on_string}: SNPs"/>
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100 <data name="blast" format="tabular" from_work_dir="output_blast.txt" label="${tool.name} on ${on_string}: BLAST alignment"/>
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101 <data name="alignment" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}: BWA alignment"/>
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102 <data name="log" format="text" from_work_dir="output.log" label="${tool.name} on ${on_string}: log">
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103 <filter>include_log</filter>
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104 </data>
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105 </outputs>
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106 <tests>
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107 <test>
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108 <param name="reference" value="Tn4401b-1.fasta" />
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109 <conditional name="collection_paired">
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110 <param name="selector" value="paired" />
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111 <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" />
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112 <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" />
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113 </conditional>
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114 <output name="summary" file="output_summary_1.txt" />
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115 </test>
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116 <test>
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117 <param name="reference" value="Tn4401b-1.fasta" />
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118 <conditional name="collection_paired">
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119 <param name="selector" value="paired" />
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120 <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" />
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121 <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" />
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122 </conditional>
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123 <conditional name="snp_profiles_source">
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124 <param name="snp_profiles_source_selector" value="history" />
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125 <param name="snp_profiles" value="Tn4401b_snp_profiles.txt" />
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126 </conditional>
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127 <conditional name="struct_profiles_source">
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128 <param name="struct_profiles_source_selector" value="history" />
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129 <param name="struct_profiles" value="Tn4401b_struct_profiles.txt" />
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130 </conditional>
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131 <output name="summary" file="output_summary_2.txt" />
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132 </test>
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133 <test>
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134 <param name="reference" value="Tn4401b-1.fasta" />
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135 <conditional name="collection_paired">
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136 <param name="selector" value="paired" />
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137 <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" />
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138 <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" />
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139 </conditional>
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140 <conditional name="snp_profiles_source">
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141 <param name="snp_profiles_source_selector" value="tool_data_table" />
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142 <param name="snp_profiles" value="Tn4401b_snp_profiles" />
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143 </conditional>
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144 <conditional name="struct_profiles_source">
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145 <param name="struct_profiles_source_selector" value="tool_data_table" />
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146 <param name="struct_profiles" value="Tn4401b_struct_profiles" />
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147 </conditional>
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148 <output name="summary" file="output_summary_2.txt" />
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149 </test>
0
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150 </tests>
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151 <help>
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152 <![CDATA[
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153 **What it does**
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154
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155 TETyper is designed for typing a specific transposable element (TE) of interest from paired-end sequencing data. It determines single nucleotide variants (SNVs) and deletions within the TE, as well as flanking sequences surrounding the TE.
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156
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157 **Input**
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158
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159 **SNP Profiles**: A tab-delimited file with the following columns:
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160
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161 1. Profile ID
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162 2. Homozygous SNPs
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163 3. Heterozygous SNPs
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164
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165 SNPs are represented in the format [REF][POSITION][ALT], and separated by pipe (`|`) characters. SNPs should be ordered by position. Valid alt-bases for heterozygous SNPs are: `M,R,W,S,Y,K`
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166
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167 For example:
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168
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169 ::
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170
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171 1 none none
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172 2 C8015T none
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173 3 C8015T|T9621C none
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174 4 T7199A|C8015T|T9621C none
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175 6 C7509G|T7917G none
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176 N2 none C8015Y
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177 N4 none A5178R
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178 N5 none C8015Y|T9663Y
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179
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180 **Structural Variant Profiles**: A tab-delimited file with the following columns:
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181
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182 1. Profile ID
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183 2. Structural Variants
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184
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185 Structural Variants are represented in the format [START-POSITION]-[END-POSITION], and separated by pipe (`|`) characters.
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186
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187 For example:
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188
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189 ::
14
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190
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191 Tn4401b none
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192 Tn4401a 7020-7118
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193 Tn4401h 6919-7106
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194 Tn4401_truncC 1-7127|9198-10006
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195
0
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196 **Output**
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197
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198 TETyper will produce a tab-seperated output file with the following outputs:
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199
7
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200 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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201 | Column | Description |
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202 +==========================+==================================================================================================================================================================================================================================================+
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203 | Deletions | A list of sequence ranges corresponding to regions of the reference classified as deletions for this sample, or "none" for no deletions. |
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204 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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205 | Structural_variant | If --struct_profiles is specified and the pattern of deletions above corresponds to one of these profiles, then the profile name is given, otherwise "unknown". |
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206 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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207 | SNPs_homozygous | A list of homozygous SNPs identified, or "none". |
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208 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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209 | SNPs_heterozygous | A list of heterozygous SNPs identified, or "none". |
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210 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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211 | Heterozygous_SNP_counts | For each heterozygous SNP, the number of reads supporting the reference and alternative calls, or "none" if there are no heterozygous SNPs. |
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212 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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213 | SNP_variant | If --snp_profiles is specified and the pattern of homozygous and heterozygous SNPs corresponds to one of these profiles, then the profile name is given. Otherwise "unknown". |
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214 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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215 | Combined_variant | Single name combining Structural_variant and SNP_variant, separated by "-". |
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216 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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217 | Left_flanks | A list of distinct sequences passing quality filters that flank the start position of the reference. |
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218 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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219 | Right_flanks | A list of distinct sequences passing quality filters that flank the end position of the reference. |
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220 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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221 | Left_flank_counts | The number of high quality reads supporting each of the left flanking sequences. |
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222 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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223 | Right_flank_counts | The number of high quality reads supporting each of the right flanking sequences. |
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224 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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225 | X_Y_presence | If --show_region is specified as --show_region X-Y, this column shows 1 if the entirety of that region is classified as present (i.e. no overlap with deleted regions), or 0 otherwise. If --show_region is unspecified, this column is omitted. |
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226 +--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
0
481b5fc3a79a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit f07bc53dc1dffac1d5a7d93d5052d8b2b9c8ad5a-dirty"
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227
481b5fc3a79a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit f07bc53dc1dffac1d5a7d93d5052d8b2b9c8ad5a-dirty"
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228 ]]>
481b5fc3a79a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit f07bc53dc1dffac1d5a7d93d5052d8b2b9c8ad5a-dirty"
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229 </help>
481b5fc3a79a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit f07bc53dc1dffac1d5a7d93d5052d8b2b9c8ad5a-dirty"
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230 <citations>
481b5fc3a79a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit f07bc53dc1dffac1d5a7d93d5052d8b2b9c8ad5a-dirty"
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231 <citation type="doi">10.1099/mgen.0.000232</citation>
481b5fc3a79a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit f07bc53dc1dffac1d5a7d93d5052d8b2b9c8ad5a-dirty"
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232 </citations>
481b5fc3a79a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit f07bc53dc1dffac1d5a7d93d5052d8b2b9c8ad5a-dirty"
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233 </tool>