Mercurial > repos > iuc > vsnp_build_tables

annotate vsnp_build_tables.xml @ 8:e54b96acea98 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
author iuc
date Tue, 16 Nov 2021 08:29:11 +0000
parents 8a7fae0cccfc
children 25714108bb22
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1 <tool id="vsnp_build_tables" name="vSNP: build tables" version="@WRAPPER_VERSION@.2" profile="@PROFILE@">
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2 <description></description>
1
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
0
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6 <requirements>
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7 <requirement type="package" version="1.76">biopython</requirement>
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8 <requirement type="package" version="0.25.3">pandas</requirement>
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9 <requirement type="package" version="1.2.8">xlsxwriter</requirement>
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10 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
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12 #import re
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efb86aade548 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2e312886647244b416c64eca91e1a61dd1be939b"
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14 mkdir 'output_excel_dir' &&
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efb86aade548 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2e312886647244b416c64eca91e1a61dd1be939b"
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16 ## The input_snps_json and input_avg_mq_json identifiers
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17 ## are typically the same string, so we append a uniquq
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18 ## extension to enable the links.
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19 #set input_snps_json_identifier = re.sub('[^\s\w\-]', '_', str($input_snps_json.element_identifier)) + '.snps'
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20 ln -s '${input_snps_json}' '${input_snps_json_identifier}' &&
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21 #set input_avg_mq_json_identifier = re.sub('[^\s\w\-]', '_', str($input_avg_mq_json.element_identifier)) + '.avg_mq'
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22 ln -s '${input_avg_mq_json}' '${input_avg_mq_json_identifier}' &&
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23 #set input_newick_identifier = re.sub('[^\s\w\-]', '_', str($input_newick.element_identifier))
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24 ln -s '${input_newick}' '${input_newick_identifier}' &&
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25
0
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26 python '$__tool_directory__/vsnp_build_tables.py'
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27 --input_snps_json '${input_snps_json_identifier}'
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28 --input_avg_mq_json '${input_avg_mq_json_identifier}'
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29 --input_newick '${input_newick_identifier}'
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30 #if str($gbk_cond.gbk_param) == 'yes':
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31 #if str($gbk_cond.gbk_source_cond.gbk_source) == 'cached':
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32 --gbk_file '$gbk_cond.gbk_source_cond.gbk_file.fields.path'
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33 #else:
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34 --gbk_file '$gbk_cond.gbk_source_cond.gbk_file'
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35 #end if
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36 #end if
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37 ]]></command>
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38 <inputs>
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39 <param name="input_snps_json" type="data" format="json" label="SNPs json file"/>
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40 <param name="input_avg_mq_json" type="data" format="json" label="Average MQ json file"/>
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41 <param name="input_newick" type="data" format="newick" label="Best-scoring ML tree file"/>
0
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42 <conditional name="gbk_cond">
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43 <param name="gbk_param" type="select" label="Use Genbank file?">
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44 <option value="yes" selected="true">yes</option>
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45 <option value="no">No</option>
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46 </param>
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47 <when value="yes">
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48 <conditional name="gbk_source_cond">
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49 <param name="gbk_source" type="select" label="Choose the source for the Genbank file">
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50 <option value="cached" selected="true">locally cached</option>
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51 <option value="history">from history</option>
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52 </param>
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53 <when value="cached">
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54 <param name="gbk_file" type="select" label="Genbank file">
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55 <options from_data_table="vsnp_genbank">
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56 <filter type="data_meta" column="0" key="dbkey" ref="input_avg_mq_json"/>
4
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57 <validator type="no_options" message="A cached Genbank file is not available for the build associated with the selected average MQ json file"/>
0
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58 </options>
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59 </param>
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60 </when>
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61 <when value="history">
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62 <param name="gbk_file" type="data" format="genbank" label="Genbank file"/>
0
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63 </when>
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64 </conditional>
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65 </when>
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66 <when value="no"/>
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67 </conditional>
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68 </inputs>
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69 <outputs>
4
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70 <collection name="excel" type="list" label="${tool.name} on ${on_string}">
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71 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;xlsx)" directory="output_excel_dir"/>
0
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72 </collection>
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73 </outputs>
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74 <tests>
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75 <test>
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76 <param name="input_snps_json" value="input_snps_json.json" ftype="json" dbkey="89"/>
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77 <param name="input_newick" value="input_newick.newick" ftype="newick" dbkey="89"/>
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78 <param name="input_avg_mq_json" value="input_avg_mq_json.json" ftype="json" dbkey="89"/>
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79 <param name="gbk_param" value="no"/>
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80 <output_collection name="excel" type="list" count="2">
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81 <element name="input_newick_newick_cascade_table" file="cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
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82 <element name="input_newick_newick_sort_table" file="sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
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83 </output_collection>
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84 </test>
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85 <test>
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86 <param name="input_snps_json" value="Mbovis-01_snps.json" ftype="json" dbkey="89"/>
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87 <param name="input_newick" value="Mbovis-01_snps.newick" ftype="newick" dbkey="89"/>
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88 <param name="input_avg_mq_json" value="Mbovis-01_avg_mq.json" ftype="json" dbkey="89"/>
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89 <param name="gbk_param" value="no"/>
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90 <output_collection name="excel" type="list" count="2">
6
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91 <element name="Mbovis-01_snps_newick_cascade_table" file="Mbovis-01_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
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92 <element name="Mbovis-01_snps_newick_sort_table" file="Mbovis-01_sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
0
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93 </output_collection>
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94 </test>
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95 <test>
4
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96 <param name="input_snps_json" value="Mbovis-01D_snps.json" ftype="json" dbkey="89"/>
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97 <param name="input_newick" value="Mbovis-01D_snps.newick" ftype="newick" dbkey="89"/>
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98 <param name="input_avg_mq_json" value="Mbovis-01D_avg_mq.json" ftype="json" dbkey="89"/>
0
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99 <param name="gbk_param" value="no"/>
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100 <output_collection name="excel" type="list" count="2">
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101 <element name="Mbovis-01D_snps_newick_cascade_table" file="Mbovis-01D_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
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102 <element name="Mbovis-01D_snps_newick_sort_table" file="Mbovis-01D_sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
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103 </output_collection>
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104 </test>
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105 <test>
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106 <param name="input_snps_json" value="Mbovis-01D6_snps.json" ftype="json" dbkey="89"/>
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107 <param name="input_newick" value="Mbovis-01D6_snps.newick" ftype="newick" dbkey="89"/>
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108 <param name="input_avg_mq_json" value="Mbovis-01D6_avg_mq.json" ftype="json" dbkey="89"/>
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109 <param name="gbk_param" value="no"/>
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110 <output_collection name="excel" type="list" count="2">
6
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111 <element name="Mbovis-01D6_snps_newick_cascade_table" file="Mbovis-01D6_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
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112 <element name="Mbovis-01D6_snps_newick_sort_table" file="Mbovis-01D6_sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
0
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113 </output_collection>
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114 </test>
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115 </tests>
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116 <help>
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117 **What it does**
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118
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119 Accepts a combination of single SNPs json, average MQ json and newick files (or associated collections of
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120 each) to produce annotated SNPs tables in the form of Excel spreadsheets. The SNPs json and average MQ json
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121 files are typically produced by the **vSNP: get SNPs** tool and the newick files are typically produced by
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122 the **Phyogenetic reconstruction with RaXML** tool.
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123
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124 The SNPs tables display closely related isolates and enables identification of mixed SNPs when multiple
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125 bacterial strains are infecting an organism. The table structure is shown below. The columns identify the
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126 genome location of the SNP calls and the isolates are contained within the rows. The reference (or ancestral
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127 strain if the reference is an outgroup) is listed across the top, identified as the "reference call". SNPs
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128 that are not highlighted will match the reference. The map-quality row values are the average of the map
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129 quality scores of each isolate in that position. These scores measure the confidence that the read has been
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130 mapped to the correct location on the genome. The maximum score possible is 60, and lower scores lessen the
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131 confidence that the SNP was correctly identified. The annotation of the position is provided at the bottom
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132 of the table.
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133
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134 .. image:: table_description.png
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135
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136 SNPs are sorted according to their evolutionary age within the table. The oldest SNPs (encompassing the most
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137 isolates) are furthest to the left. This sorting is somewhat crude - the intent is to improve readibility or
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138 more easily match a related tree.
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139
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140 For a more detailed discussion, see the **Validating and correcting SNP calls** section of
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141 the `vSNP documentation`_.
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142
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143 .. _vSNP documentation: https://github.com/USDA-VS/vSNP/blob/master/docs/detailed_usage.md
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144
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145 **Required Options**
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146
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147 * **Use Genbank file** - Select "yes" to annotate the tables using the information in the Genbank file. Locally cached files, if available, provide the most widely used annotations, but more custom Genbank files can be chosen from the current history.
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148 </help>
1
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149 <expand macro="citations"/>
0
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150 </tool>
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151