Mercurial > repos > iuc > vsnp_get_snps

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
author iuc
date Fri, 10 Jun 2022 06:08:49 +0000
parents ae7b1b97a2a0
children
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4
4535ad8b74f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
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1 <tool id="vsnp_get_snps" name="vSNP: get SNPs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
1
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7 <expand macro="openpyxl_requirement"/>
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8 <expand macro="pandas_requirement"/>
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9 <expand macro="pyvcf_requirement"/>
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10 <expand macro="xlrd_requirement"/>
0
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11 </requirements>
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12 <command detect_errors="exit_code"><![CDATA[
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13 #import re
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14
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15 #set input_vcf_dir = 'input_vcf_dir'
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16 #set output_json_avg_mq_dir = 'output_json_avg_mq_dir'
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17 #set output_json_snps_dir = 'output_json_snps_dir'
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18 #set output_snps_dir = 'output_snps_dir'
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19
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20 mkdir -p $input_vcf_dir &&
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21 mkdir -p $output_json_avg_mq_dir &&
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22 mkdir -p $output_json_snps_dir &&
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23 mkdir -p $output_snps_dir &&
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24
1
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25 #if str($input_additional_zc_vcf_collection_cond.input_additional_zc_vcf_collection) =='yes':
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26 #set dbkey = '?'
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27 #for $i in $input_additional_zc_vcf_collection_cond.input_vcf_collection:
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28 #if str($dbkey) == '?':
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29 #set dbkey = $i.metadata.dbkey
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30 #else if str($dbkey) != $i.metadata.dbkey:
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31 >&2 echo "The dbkeys associated with the zero coverage VCF files with SNPs found in closely related isolate groups are not unique, check ${i.name}" && exit 1
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32 #end if
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33 #set vcf_identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
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34 ln -s '${i}' '$input_vcf_dir/${vcf_identifier}' &&
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35 #end for
0
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36 #if str($dbkey) == '?':
1
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37 >&2 echo "The dbkey must be set for the zero coverage VCF files with SNPs found in closely related isolate groups" && exit 1
0
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38 #end if
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39 #end if
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40 #if str($input_zc_vcf_type_cond.input_zc_vcf_type) == "single":
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41 #set zc_vcf_identifier = re.sub('[^\s\w\-]', '_', str($input_zc_vcf.element_identifier))
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42 ln -s '${input_zc_vcf}' '$input_vcf_dir/${zc_vcf_identifier}' &&
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43 #else
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44 #for $i in $input_zc_vcf_type_cond.input_zc_vcf_collection:
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45 #set zc_vcf_identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
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46 ln -s '${i}' '$input_vcf_dir/${zc_vcf_identifier}' &&
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47 #end for
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48 #end if
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49 #if str($input_excel_cond.input_excel_param) == 'yes':
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50 #if str($input_excel_cond.excel_source_cond.excel_source) == 'cached':
3
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51 ## The selected Excel filter must be associated with the dbkey value defined above.
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52 #set excel_file = $input_excel_cond.excel_source_cond.input_excel.fields.path
0
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53 #else:
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54 #set excel_file = $input_excel_cond.excel_source_cond.input_excel
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55 #end if
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56 #end if
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57 python '$__tool_directory__/vsnp_get_snps.py'
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58 --ac $ac
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59 #if str($input_excel_cond.input_excel_param) == 'yes':
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60 --input_excel '$excel_file'
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61 #end if
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62 $all_isolates
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63 --input_vcf_dir '$input_vcf_dir'
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64 --min_mq $min_mq
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65 --min_quality_score $min_quality_score
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66 --output_json_avg_mq_dir '$output_json_avg_mq_dir'
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67 --output_json_snps_dir '$output_json_snps_dir'
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68 --output_snps_dir '$output_snps_dir'
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69 --output_summary '$output_summary'
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70 --processes \${GALAXY_SLOTS:-8}
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71 --quality_score_n_threshold $quality_score_n_threshold
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72 --dbkey '$dbkey'
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73 ]]></command>
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74 <inputs>
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75 <conditional name="input_zc_vcf_type_cond">
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76 <param name="input_zc_vcf_type" type="select" label="Choose the category of the files to be analyzed">
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77 <option value="collection" selected="true">A collection of zero coverage VCF files</option>
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78 <option value="single">A single zero coverage VCF file</option>
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79 </param>
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80 <when value="single">
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81 <param name="input_zc_vcf" type="data" format="vcf" label="Zero coverage VCF file"/>
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82 </when>
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83 <when value="collection">
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84 <param name="input_zc_vcf_collection" format="vcf" type="data_collection" collection_type="list" label="Collection of zero coverage VCF files"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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parents:
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85 </when>
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86 </conditional>
1
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parents: 0
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87 <conditional name="input_additional_zc_vcf_collection_cond">
9ac0b1d5560d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
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parents: 0
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88 <param name="input_additional_zc_vcf_collection" type="select" label="Include an additional collection of curated zero-coverage VCF files?">
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parents: 0
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89 <option value="no" selected="true">No</option>
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parents: 0
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90 <option value="yes">Yes</option>
9ac0b1d5560d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
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parents: 0
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91 </param>
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parents: 0
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92 <when value="no"/>
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parents: 0
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93 <when value="yes">
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parents: 0
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94 <param name="input_vcf_collection" format="vcf" type="data_collection" collection_type="list" label="Collection of zero coverage VCF files with SNPs found in closely related isolate groups"/>
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parents: 0
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95 </when>
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parents: 0
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96 </conditional>
0
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97 <param name="ac" type="integer" min="0" value="2" label="Allele count threshold" help="At least 1 position must have this value for a SNP to be added to a group"/>
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98 <param name="min_mq" type="integer" min="0" value="56" label="Map quality threshold" help="At least 1 position must have a higher MQ value for a SNP to be added to a group"/>
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99 <param name="min_quality_score" type="integer" min="0" value="150" label="Quality score threshold" help="At least 1 position must have a higher quality score for a SNP to be added to a group"/>
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100 <param name="quality_score_n_threshold" type="integer" min="0" value="150" label="Minimum quality score N value for alleles" help="Alleles are marked as N for quality scores between this value and the minimum quality score value above"/>
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101 <conditional name="input_excel_cond">
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102 <param name="input_excel_param" type="select" label="Use Excel file for grouping and filtering?">
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103 <option value="yes" selected="true">Yes</option>
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104 <option value="no">No</option>
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105 </param>
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parents:
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106 <when value="yes">
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107 <conditional name="excel_source_cond">
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108 <param name="excel_source" type="select" label="Choose the source for the Excel file">
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109 <option value="cached">locally cached</option>
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110 <option value="history">from history</option>
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111 </param>
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parents:
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112 <when value="cached">
3
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parents: 1
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113 <param name="input_excel" type="select" label="Excel file" help="Select the file associated with the same dbkey as the input VCF file(s)">
0
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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114 <options from_data_table="vsnp_excel">
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115 <validator type="no_options" message="No built-in Excel grouping and filtering datasets are available"/>
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116 </options>
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117 </param>
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118 </when>
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119 <when value="history">
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120 <param name="input_excel" type="data" format="xlsx" label="Excel file"/>
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121 </when>
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122 </conditional>
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123 </when>
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124 <when value="no"/>
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125 </conditional>
1
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parents: 0
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126 <param name="all_isolates" type="boolean" truevalue="--all_isolates" falsevalue="" checked="true" label="Create a group containing all isolates?"/>
0
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127 </inputs>
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128 <outputs>
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129 <collection name="snps" type="list" label="${tool.name} on ${on_string} (SNPs)">
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130 <discover_datasets pattern="__name_and_ext__" directory="output_snps_dir"/>
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131 </collection>
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132 <collection name="json_avg_mq" type="list" label="${tool.name} on ${on_string} (average mq)">
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133 <discover_datasets pattern="__name_and_ext__" directory="output_json_avg_mq_dir"/>
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134 </collection>
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135 <collection name="json_snps" type="list" label="${tool.name} on ${on_string} (SNPs as json)">
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136 <discover_datasets pattern="__name_and_ext__" directory="output_json_snps_dir"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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137 </collection>
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138 <data name="output_summary" format="html" label="${tool.name} on ${on_string} (summary)"/>
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139 </outputs>
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140 <tests>
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141 <!--
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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142 Unfortunately the test files cannot be gzipped since Galaxy changes the file names
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143 to be something like 00-0121_WI_Cervid_99-A_vcf_gz, and the VCF Reader requires
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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144 gzipped files to have a .gz extension. The exception is
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145 UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
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146 -->
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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147 <!-- A single vcf input, no excel file, all_isolates is False -->
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148 <test expect_num_outputs="4">
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149 <param name="input_zc_vcf_type" value="single"/>
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150 <param name="input_zc_vcf" value="input_zc_vcf.vcf" ftype="vcf" dbkey="89"/>
1
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parents: 0
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151 <param name="input_additional_zc_vcf_collection" value="yes"/>
0
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152 <param name="input_vcf_collection">
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153 <collection type="list">
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154 <element name="SRR8073662_zc.vcf" value="SRR8073662_zc.vcf" dbkey="89"/>
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155 <element name="SRR1792272_zc.vcf" value="SRR1792272_zc.vcf" dbkey="89"/>
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156 </collection>
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157 </param>
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158 <param name="input_excel_param" value="no"/>
1
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parents: 0
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159 <param name="all_isolates" value=""/>
0
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160 <output_collection name="snps" type="list" count="1">
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161 <element name="all_vcf" ftype="fasta">
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162 <assert_contents>
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163 <has_size value="150"/>
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164 </assert_contents>
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165 </element>
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166 </output_collection>
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parents:
diff changeset
167 <output_collection name="json_avg_mq" type="list" count="1">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
168 <element name="all_vcf" ftype="json">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
169 <assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
170 <has_size value="551"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
171 </assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
172 </element>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
173 </output_collection>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
174 <output_collection name="json_snps" type="list" count="1">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
175 <element name="all_vcf" ftype="json">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
176 <assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
177 <has_size value="876"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
178 </assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
179 </element>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
180 </output_collection>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
181 <output name="output_summary" ftype="html">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
182 <assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
183 <has_size value="303"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
184 </assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
185 </output>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
186 </test>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
187 <!-- An input collection, no excel file, all_isolates is False -->
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
188 <test expect_num_outputs="4">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
189 <param name="input_zc_vcf_type" value="collection"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
190 <param name="input_zc_vcf_collection">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
191 <collection type="list">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
192 <element name="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" value="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" dbkey="89"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
193 <element name="BCG_Tokyo_Unknown_JP_DRR029468.vcf" value="BCG_Tokyo_Unknown_JP_DRR029468.vcf" dbkey="89"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
194 </collection>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
195 </param>
1
9ac0b1d5560d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 0
diff changeset
196 <param name="input_additional_zc_vcf_collection" value="yes"/>
0
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
197 <param name="input_vcf_collection">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
198 <collection type="list">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
199 <element name="01_1787_FL_Zoo_Jaguar.vcf" value="01_1787_FL_Zoo_Jaguar.vcf" dbkey="89"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
200 <element name="02_5877_MEX_TX_Fed.vcf" value="02_5877_MEX_TX_Fed.vcf" dbkey="89"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
201 <element name="02_0585_COA_TX_Fed.vcf" value="02_0585_COA_TX_Fed.vcf" dbkey="89"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
202 </collection>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
203 </param>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
204 <param name="input_excel_param" value="no"/>
1
9ac0b1d5560d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 0
diff changeset
205 <param name="all_isolates" value=""/>
0
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
206 <output_collection name="snps" type="list" count="1">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
207 <element name="all_vcf" ftype="fasta">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
208 <assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
209 <has_size value="5226"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
210 </assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
211 </element>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
212 </output_collection>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
213 <output_collection name="json_avg_mq" type="list" count="1">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
214 <element name="all_vcf" ftype="json">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
215 <assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
216 <has_size value="24332"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
217 </assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
218 </element>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
219 </output_collection>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
220 <output_collection name="json_snps" type="list" count="1">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
221 <element name="all_vcf" ftype="json">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
222 <assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
223 <has_size value="38798"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
224 </assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
225 </element>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
226 </output_collection>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
227 <output name="output_summary" ftype="html">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
228 <assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
229 <has_size value="303"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
230 </assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
231 </output>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
232 </test>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
233 <!-- An input collection, an excel file, all_isolates is False -->
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
234 <test expect_num_outputs="4">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
235 <param name="input_zc_vcf_type" value="collection"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
236 <param name="input_zc_vcf_collection">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
237 <collection type="list">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
238 <element name="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" value="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" dbkey="89"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
239 <element name="BCG_Tokyo_Unknown_JP_DRR029468.vcf" value="BCG_Tokyo_Unknown_JP_DRR029468.vcf" dbkey="89"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
240 </collection>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
241 </param>
1
9ac0b1d5560d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 0
diff changeset
242 <param name="input_additional_zc_vcf_collection" value="yes"/>
0
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
243 <param name="input_vcf_collection">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
244 <collection type="list">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
245 <element name="01_1787_FL_Zoo_Jaguar.vcf" value="01_1787_FL_Zoo_Jaguar.vcf" dbkey="89"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
246 <element name="02_5877_MEX_TX_Fed.vcf" value="02_5877_MEX_TX_Fed.vcf" dbkey="89"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
247 <element name="02_0585_COA_TX_Fed.vcf" value="02_0585_COA_TX_Fed.vcf" dbkey="89"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
248 </collection>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
249 </param>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
250 <param name="input_excel_param" value="yes"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
251 <param name="input_excel" value="89"/>
1
9ac0b1d5560d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 0
diff changeset
252 <param name="all_isolates" value=""/>
0
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
253 <output_collection name="snps" type="list" count="1">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
254 <element name="Mbovis-17" ftype="fasta">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
255 <assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
256 <has_size value="749"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
257 </assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
258 </element>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
259 </output_collection>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
260 <output_collection name="json_avg_mq" type="list" count="1">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
261 <element name="Mbovis-17" ftype="json">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
262 <assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
263 <has_size value="10884"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
264 </assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
265 </element>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
266 </output_collection>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
267 <output_collection name="json_snps" type="list" count="1">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
268 <element name="Mbovis-17" ftype="json">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
269 <assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
270 <has_size value="6396"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
271 </assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
272 </element>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
273 </output_collection>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
274 <output name="output_summary" ftype="html">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
275 <assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
276 <has_size value="1057"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
277 </assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
278 </output>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
279 </test>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
280 <!-- An input collection, an excel file, all_isolates is True -->
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
281 <test expect_num_outputs="4">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
282 <param name="input_zc_vcf_type" value="collection"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
283 <param name="input_zc_vcf_collection">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
284 <collection type="list">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
285 <element name="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" value="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" dbkey="89"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
286 <element name="BCG_Tokyo_Unknown_JP_DRR029468.vcf" value="BCG_Tokyo_Unknown_JP_DRR029468.vcf" dbkey="89"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
287 </collection>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
288 </param>
1
9ac0b1d5560d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 0
diff changeset
289 <param name="input_additional_zc_vcf_collection" value="yes"/>
0
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
290 <param name="input_vcf_collection">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
291 <collection type="list">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
292 <element name="01_1787_FL_Zoo_Jaguar.vcf" value="01_1787_FL_Zoo_Jaguar.vcf" dbkey="89"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
293 <element name="02_5877_MEX_TX_Fed.vcf" value="02_5877_MEX_TX_Fed.vcf" dbkey="89"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
294 <element name="02_0585_COA_TX_Fed.vcf" value="02_0585_COA_TX_Fed.vcf" dbkey="89"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
295 </collection>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
296 </param>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
297 <param name="input_excel_param" value="yes"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
298 <param name="input_excel" value="89"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
299 <param name="all_isolates" value="--all_isolates"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
300 <output_collection name="snps" type="list" count="2">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
301 <element name="Mbovis-17" ftype="fasta">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
302 <assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
303 <has_size value="749"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
304 </assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
305 </element>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
306 <element name="all_vcf" ftype="fasta">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
307 <assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
308 <has_size value="4920"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
309 </assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
310 </element>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
311 </output_collection>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
312 <output_collection name="json_avg_mq" type="list" count="2">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
313 <element name="Mbovis-17" ftype="json">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
314 <assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
315 <has_size value="10884"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
316 </assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
317 </element>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
318 <element name="all_vcf" ftype="json">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
319 <assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
320 <has_size value="24332"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
321 </assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
322 </element>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
323 </output_collection>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
324 <output_collection name="json_snps" type="list" count="2">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
325 <element name="Mbovis-17" ftype="json">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
326 <assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
327 <has_size value="6396"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
328 </assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
329 </element>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
330 <element name="all_vcf" ftype="json">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
331 <assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
332 <has_size value="36466"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
333 </assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
334 </element>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
335 </output_collection>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
336 <output name="output_summary" ftype="html">
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
337 <assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
338 <has_size value="1056"/>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
339 </assert_contents>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
340 </output>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
341 </test>
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents:
diff changeset
342 </tests>
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343 <help>
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344 **What it does**
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345
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346 Accepts a zero coverage VCF file produced by the **vSNP: add zero coverage** tool (or a collection of them) along with a collection
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347 of zero coverage VCF files that have been aligned with the same reference and contain SNPs called between closely related isolate groups.
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348 The tool produces fasta files containing SNP alignments, json files containing the SNP positions and additional json files containing
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349 the average map quality values.
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350
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351 The SNP alignments produced by this tool are used to create phylogenetic trees, so larger input collections result in more populated
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352 phylogenetic trees. Both of the json outputs are used by the **vSNP: build tables** tool to produce annotated SNP tables in the form
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353 of Excel spreadsheets.
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354
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355 An Excel spreadsheet containing specified SNPs can optiomally be used to filter desired SNP positions by group. Users can choose a
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356 locally cached Excel spreadsheet or one from their current history.
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357
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358 A SNP is added to a group if it has at least one position with a specified allele count value, a quality score greater than a specified
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359 value, and a map quality greater than a specified value.
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360
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361 If the allele count equals the specified value (2) and the quality score for a SNP position is greater than the minimum quality score
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362 value (150), the alternate allele is called.
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363
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364 However, if the allele count is 1, the position is called ambiguous. Deletions are called when the alternate allele is a gap. If the
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365 quality score is less than or equal to the minimum quality score N value for alleles (150), the allele is marked "N".
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366
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367 **Required Options**
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368
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369 * **Zero coverage VCF file(s)** - Select a single or collection of zero coverage VCF files, typically produced by the **vSNP: add zero coverage** tool, from the current history.
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370 * **Collection of zero coverage VCF files with SNPs found in closely related isolate groups** - Select a dataset collection of zero coverage vcf files from the current history.
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371
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372 **Additional Options**
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373
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374 * **Allele count threshold** - At least 1 position must have an allele count greater than this value for a SNP to be added to a group (2 is optimal).
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375 * **Map quality threshold** - At least 1 position must have a higher MQ value for a SNP to be added to a group (56 is optimal).
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376 * **Quality score threshold** -At least 1 position must have a higher quality score for a SNP to be added to a group (150 is optimal).
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377 * **Minimum quality score N value for alleles** - If none of the avove 3 requirements is met and the quality score is less than or equal to the minimum quality score N value for alleles, the allele is marked "N" (150 is optimal).
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378 * **Use Excel file for grouping and filtering?** - select Yes to filter desired SNP positions by group. A cached Excel spreadsheet provides the most widely used SNP positions for grouping, but a custom spreadhseet can be selected from the current history.
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379 * **Create a group containing all isolates?** - select Yes to output an additional group containing of all isolates.
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380 </help>
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381 <expand macro="citations"/>
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382 </tool>
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383