Mercurial > repos > greg > vsnp_get_snps

annotate vsnp_get_snps.xml @ 13:cd636b0e4f95 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit cab8ee43e902a3ae7b0fd6b06842c4b5c221af25"
author greg
date Tue, 21 Sep 2021 00:21:36 +0000
parents 544b2ed99a9a
children 44b84d32883c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
10
be5875f29ea4 Uploaded
greg
parents: 9
diff changeset
1 <tool id="vsnp_get_snps" name="vSNP: get SNPs" version="@WRAPPER_VERSION@.1+galaxy0" profile="@PROFILE@">
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
2 <description></description>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
3 <macros>
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
4 <import>macros.xml</import>
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
5 </macros>
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
6 <requirements>
10
be5875f29ea4 Uploaded
greg
parents: 9
diff changeset
7 <expand macro="openpyxl_requirement"/>
be5875f29ea4 Uploaded
greg
parents: 9
diff changeset
8 <expand macro="pandas_requirement"/>
be5875f29ea4 Uploaded
greg
parents: 9
diff changeset
9 <expand macro="pyvcf_requirement"/>
be5875f29ea4 Uploaded
greg
parents: 9
diff changeset
10 <expand macro="xlrd_requirement"/>
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
11 </requirements>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
12 <command detect_errors="exit_code"><![CDATA[
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
13 #import re
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
14
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
15 #set input_vcf_dir = 'input_vcf_dir'
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
16 #set output_json_avg_mq_dir = 'output_json_avg_mq_dir'
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
17 #set output_json_snps_dir = 'output_json_snps_dir'
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
18 #set output_snps_dir = 'output_snps_dir'
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
19
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
20 mkdir -p $input_vcf_dir &&
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
21 mkdir -p $output_json_avg_mq_dir &&
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
22 mkdir -p $output_json_snps_dir &&
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
23 mkdir -p $output_snps_dir &&
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
24
12
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
25 #if str($input_additional_zc_vcf_collection_cond.input_additional_zc_vcf_collection) =='yes':
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
26 #set dbkey = '?'
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
27 #for $i in $input_additional_zc_vcf_collection_cond.input_vcf_collection:
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
28 #if str($dbkey) == '?':
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
29 #set dbkey = $i.metadata.dbkey
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
30 #else if str($dbkey) != $i.metadata.dbkey:
13
cd636b0e4f95 "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit cab8ee43e902a3ae7b0fd6b06842c4b5c221af25"
greg
parents: 12
diff changeset
31 >&2 echo "The dbkeys associated with the zero coverage VCF files with SNPs found in closely related isolate groups are not unique, check ${i.name}" && exit 1
12
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
32 #end if
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
33 #set vcf_identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
34 ln -s '${i}' '$input_vcf_dir/${vcf_identifier}' &&
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
35 #end for
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
36 #if str($dbkey) == '?':
12
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
37 >&2 echo "The dbkey must be set for the zero coverage VCF files with SNPs found in closely related isolate groups" && exit 1
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
38 #end if
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
39 #end if
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
40 #if str($input_zc_vcf_type_cond.input_zc_vcf_type) == "single":
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
41 #set zc_vcf_identifier = re.sub('[^\s\w\-]', '_', str($input_zc_vcf.element_identifier))
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
42 ln -s '${input_zc_vcf}' '$input_vcf_dir/${zc_vcf_identifier}' &&
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
43 #else
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
44 #for $i in $input_zc_vcf_type_cond.input_zc_vcf_collection:
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
45 #set zc_vcf_identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
46 ln -s '${i}' '$input_vcf_dir/${zc_vcf_identifier}' &&
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
47 #end for
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
48 #end if
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
49 #if str($input_excel_cond.input_excel_param) == 'yes':
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
50 #if str($input_excel_cond.excel_source_cond.excel_source) == 'cached':
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
51 #set excel_file = 'No genome specified for input VCF (database) file(s)'
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
52 #set excel_fields = $__app__.tool_data_tables['vsnp_excel'].get_fields()
10
be5875f29ea4 Uploaded
greg
parents: 9
diff changeset
53 ## The value of excel_fields is a nested list that looks like this.
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
54 ## [['AF2122', 'Mbovis_define_filter.xlsx', '~/tool-data/vsnp/AF2122/excel/Mbovis_define_filter.xlsx', 'Excel file for AF2122'],...]
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
55 #for $i in $excel_fields:
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
56 #if str($i[0]) == $dbkey:
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
57 #set excel_file = $i[2]
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
58 #break
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
59 #end if
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
60 #end for
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
61 #else:
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
62 #set excel_file = $input_excel_cond.excel_source_cond.input_excel
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
63 #end if
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
64 #end if
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
65 python '$__tool_directory__/vsnp_get_snps.py'
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
66 --ac $ac
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
67 #if str($input_excel_cond.input_excel_param) == 'yes':
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
68 --input_excel '$excel_file'
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
69 #end if
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
70 $all_isolates
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
71 --input_vcf_dir '$input_vcf_dir'
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
72 --min_mq $min_mq
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
73 --min_quality_score $min_quality_score
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
74 --output_json_avg_mq_dir '$output_json_avg_mq_dir'
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
75 --output_json_snps_dir '$output_json_snps_dir'
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
76 --output_snps_dir '$output_snps_dir'
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
77 --output_summary '$output_summary'
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
78 --processes \${GALAXY_SLOTS:-8}
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
79 --quality_score_n_threshold $quality_score_n_threshold
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
80 --dbkey '$dbkey'
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
81 ]]></command>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
82 <inputs>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
83 <conditional name="input_zc_vcf_type_cond">
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
84 <param name="input_zc_vcf_type" type="select" label="Choose the category of the files to be analyzed">
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
85 <option value="collection" selected="true">A collection of zero coverage VCF files</option>
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
86 <option value="single">A single zero coverage VCF file</option>
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
87 </param>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
88 <when value="single">
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
89 <param name="input_zc_vcf" type="data" format="vcf" label="Zero coverage VCF file"/>
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
90 </when>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
91 <when value="collection">
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
92 <param name="input_zc_vcf_collection" format="vcf" type="data_collection" collection_type="list" label="Collection of zero coverage VCF files"/>
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
93 </when>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
94 </conditional>
12
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
95 <conditional name="input_additional_zc_vcf_collection_cond">
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
96 <param name="input_additional_zc_vcf_collection" type="select" label="Include an additional collection of curated zero-coverage VCF files?">
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
97 <option value="no" selected="true">No</option>
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
98 <option value="yes">Yes</option>
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
99 </param>
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
100 <when value="no"/>
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
101 <when value="yes">
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
102 <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"/>
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
103 </when>
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
104 </conditional>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
105 <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"/>
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
106 <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"/>
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
107 <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"/>
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
108 <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"/>
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
109 <conditional name="input_excel_cond">
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
110 <param name="input_excel_param" type="select" label="Use Excel file for grouping and filtering?">
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
111 <option value="yes" selected="true">Yes</option>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
112 <option value="no">No</option>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
113 </param>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
114 <when value="yes">
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
115 <conditional name="excel_source_cond">
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
116 <param name="excel_source" type="select" label="Choose the source for the Excel file">
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
117 <option value="cached">locally cached</option>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
118 <option value="history">from history</option>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
119 </param>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
120 <when value="cached">
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
121 <param name="input_excel" type="select" label="Excel file">
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
122 <options from_data_table="vsnp_excel">
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
123 <validator type="no_options" message="No built-in Excel grouping and filtering datasets are available"/>
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
124 </options>
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
125 </param>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
126 </when>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
127 <when value="history">
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
128 <param name="input_excel" type="data" format="xlsx" label="Excel file"/>
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
129 </when>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
130 </conditional>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
131 </when>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
132 <when value="no"/>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
133 </conditional>
10
be5875f29ea4 Uploaded
greg
parents: 9
diff changeset
134 <param argument="all_isolates" type="boolean" truevalue="--all_isolates" falsevalue="" checked="true" label="Create a group containing all isolates?"/>
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
135 </inputs>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
136 <outputs>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
137 <collection name="snps" type="list" label="${tool.name} on ${on_string} (SNPs)">
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
138 <discover_datasets pattern="__name_and_ext__" directory="output_snps_dir"/>
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
139 </collection>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
140 <collection name="json_avg_mq" type="list" label="${tool.name} on ${on_string} (average mq)">
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
141 <discover_datasets pattern="__name_and_ext__" directory="output_json_avg_mq_dir"/>
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
142 </collection>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
143 <collection name="json_snps" type="list" label="${tool.name} on ${on_string} (SNPs as json)">
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
144 <discover_datasets pattern="__name_and_ext__" directory="output_json_snps_dir"/>
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
145 </collection>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
146 <data name="output_summary" format="html" label="${tool.name} on ${on_string} (summary)"/>
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
147 </outputs>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
148 <tests>
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
149 <!--
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
150 Unfortunately the test files cannot be gzipped since Galaxy changes the file names
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
151 to be something like 00-0121_WI_Cervid_99-A_vcf_gz, and the VCF Reader requires
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
152 gzipped files to have a .gz extension. The exception is
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
153 UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
154 -->
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
155 <!-- A single vcf input, no excel file, all_isolates is False -->
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
156 <test expect_num_outputs="4">
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
157 <param name="input_zc_vcf_type" value="single"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
158 <param name="input_zc_vcf" value="input_zc_vcf.vcf" ftype="vcf" dbkey="89"/>
12
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
159 <param name="input_additional_zc_vcf_collection" value="yes"/>
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
160 <param name="input_vcf_collection">
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
161 <collection type="list">
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
162 <element name="SRR8073662_zc.vcf" value="SRR8073662_zc.vcf" dbkey="89"/>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
163 <element name="SRR1792272_zc.vcf" value="SRR1792272_zc.vcf" dbkey="89"/>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
164 </collection>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
165 </param>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
166 <param name="input_excel_param" value="no"/>
10
be5875f29ea4 Uploaded
greg
parents: 9
diff changeset
167 <param name="all_isolates" value=""/>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
168 <output_collection name="snps" type="list" count="1">
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
169 <element name="all_vcf" file="all_vcf.fasta" ftype="fasta" compare="contains"/>
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
170 </output_collection>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
171 <output_collection name="json_avg_mq" type="list" count="1">
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
172 <element name="all_vcf" file="json_avg_mq_all_vcf.json" ftype="json" compare="contains"/>
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
173 </output_collection>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
174 <output_collection name="json_snps" type="list" count="1">
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
175 <element name="all_vcf" file="json_all_vcf.json" ftype="json" compare="contains"/>
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
176 </output_collection>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
177 <output name="output_summary" file="output_summary.html" ftype="html" compare="contains"/>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
178 </test>
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
179 <!-- An input collection, no excel file, all_isolates is False -->
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
180 <test expect_num_outputs="4">
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
181 <param name="input_zc_vcf_type" value="collection"/>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
182 <param name="input_zc_vcf_collection">
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
183 <collection type="list">
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
184 <element name="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" value="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
185 <element name="BCG_Tokyo_Unknown_JP_DRR029468.vcf" value="BCG_Tokyo_Unknown_JP_DRR029468.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
186 </collection>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
187 </param>
12
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
188 <param name="input_additional_zc_vcf_collection" value="yes"/>
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
189 <param name="input_vcf_collection">
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
190 <collection type="list">
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
191 <element name="01_1787_FL_Zoo_Jaguar.vcf" value="01_1787_FL_Zoo_Jaguar.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
192 <element name="02_5877_MEX_TX_Fed.vcf" value="02_5877_MEX_TX_Fed.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
193 <element name="02_0585_COA_TX_Fed.vcf" value="02_0585_COA_TX_Fed.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
194 </collection>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
195 </param>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
196 <param name="input_excel_param" value="no"/>
10
be5875f29ea4 Uploaded
greg
parents: 9
diff changeset
197 <param name="all_isolates" value=""/>
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
198 <output_collection name="snps" type="list" count="1">
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
199 <element name="all_vcf" file="all_vcf2.fasta" ftype="fasta" compare="contains"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
200 </output_collection>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
201 <output_collection name="json_avg_mq" type="list" count="1">
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
202 <element name="all_vcf" file="json_avg_mq_all_vcf.json" ftype="json" compare="contains"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
203 </output_collection>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
204 <output_collection name="json_snps" type="list" count="1">
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
205 <element name="all_vcf" file="json_all_vcf.json" ftype="json" compare="contains"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
206 </output_collection>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
207 <output name="output_summary" file="output_summary2.html" ftype="html" compare="contains"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
208 </test>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
209 <!-- An input collection, an excel file, all_isolates is False -->
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
210 <test expect_num_outputs="4">
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
211 <param name="input_zc_vcf_type" value="collection"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
212 <param name="input_zc_vcf_collection">
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
213 <collection type="list">
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
214 <element name="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" value="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
215 <element name="BCG_Tokyo_Unknown_JP_DRR029468.vcf" value="BCG_Tokyo_Unknown_JP_DRR029468.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
216 </collection>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
217 </param>
12
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
218 <param name="input_additional_zc_vcf_collection" value="yes"/>
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
219 <param name="input_vcf_collection">
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
220 <collection type="list">
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
221 <element name="01_1787_FL_Zoo_Jaguar.vcf" value="01_1787_FL_Zoo_Jaguar.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
222 <element name="02_5877_MEX_TX_Fed.vcf" value="02_5877_MEX_TX_Fed.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
223 <element name="02_0585_COA_TX_Fed.vcf" value="02_0585_COA_TX_Fed.vcf" dbkey="89"/>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
224 </collection>
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
225 </param>
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
226 <param name="input_excel_param" value="yes"/>
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
227 <param name="input_excel" value="89"/>
10
be5875f29ea4 Uploaded
greg
parents: 9
diff changeset
228 <param name="all_isolates" value=""/>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
229 <output_collection name="snps" type="list" count="1">
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
230 <element name="Mbovis-17" file="Mbovis-17_snps.fasta" ftype="fasta" compare="contains"/>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
231 </output_collection>
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
232 <output_collection name="json_avg_mq" type="list" count="1">
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
233 <element name="Mbovis-17" file="Mbovis-17_avg_mq_json.json" ftype="json" compare="contains"/>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
234 </output_collection>
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
235 <output_collection name="json_snps" type="list" count="1">
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
236 <element name="Mbovis-17" file="Mbovis-17_snps_json.json" ftype="json" compare="contains"/>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
237 </output_collection>
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
238 <output name="output_summary" file="output_summary3.html" ftype="html" compare="contains"/>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
239 </test>
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
240 <!-- An input collection, an excel file, all_isolates is True -->
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
241 <test expect_num_outputs="4">
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
242 <param name="input_zc_vcf_type" value="collection"/>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
243 <param name="input_zc_vcf_collection">
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
244 <collection type="list">
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
245 <element name="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" value="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
246 <element name="BCG_Tokyo_Unknown_JP_DRR029468.vcf" value="BCG_Tokyo_Unknown_JP_DRR029468.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
247 </collection>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
248 </param>
12
544b2ed99a9a Uploaded
greg
parents: 10
diff changeset
249 <param name="input_additional_zc_vcf_collection" value="yes"/>
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
250 <param name="input_vcf_collection">
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
251 <collection type="list">
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
252 <element name="01_1787_FL_Zoo_Jaguar.vcf" value="01_1787_FL_Zoo_Jaguar.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
253 <element name="02_5877_MEX_TX_Fed.vcf" value="02_5877_MEX_TX_Fed.vcf" dbkey="89"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
254 <element name="02_0585_COA_TX_Fed.vcf" value="02_0585_COA_TX_Fed.vcf" dbkey="89"/>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
255 </collection>
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
256 </param>
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
257 <param name="input_excel_param" value="yes"/>
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
258 <param name="input_excel" value="89"/>
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
259 <param name="all_isolates" value="--all_isolates"/>
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
260 <output_collection name="snps" type="list" count="2">
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
261 <element name="Mbovis-17" file="Mbovis-17_snps.fasta" ftype="fasta" compare="contains"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
262 <element name="all_vcf" file="all_vcf2.fasta" ftype="fasta" compare="contains"/>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
263 </output_collection>
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
264 <output_collection name="json_avg_mq" type="list" count="2">
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
265 <element name="Mbovis-17" file="Mbovis-17_avg_mq_json.json" ftype="json" compare="contains"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
266 <element name="all_vcf" file="Mbovis-17_avg_mq_json.json" ftype="json" compare="contains"/>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
267 </output_collection>
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
268 <output_collection name="json_snps" type="list" count="2">
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
269 <element name="Mbovis-17" file="Mbovis-17_snps_json.json" ftype="json" compare="contains"/>
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
270 <element name="all_vcf" file="Mbovis-17_snps_json.json" ftype="json" compare="contains"/>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
271 </output_collection>
9
0fe292b20b9d "planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 3b7fef2d17fec96647345e89c774d4af417d23d7"
greg
parents: 8
diff changeset
272 <output name="output_summary" file="output_summary4.html" ftype="html" compare="contains"/>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
273 </test>
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
274 </tests>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
275 <help>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
276 **What it does**
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
277
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
278 Accepts a zero coverage VCF file produced by the **vSNP: add zero coverage** tool (or a collection of them) along with a collection
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
279 of zero coverage VCF files that have been aligned with the same reference and contain SNPs called between closely related isolate groups.
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
280 The tool produces fasta files containing SNP alignments, json files containing the SNP positions and additional json files containing
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
281 the average map quality values.
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
282
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
283 The SNP alignments produced by this tool are used to create phylogenetic trees, so larger input collections result in more populated
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
284 phylogenetic trees. Both of the json outputs are used by the **vSNP: build tables** tool to produce annotated SNP tables in the form
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
285 of Excel spreadsheets.
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
286
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
287 An Excel spreadsheet containing specified SNPs can optiomally be used to filter desired SNP positions by group. Users can choose a
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
288 locally cached Excel spreadsheet or one from their current history.
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
289
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
290 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
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
291 value, and a map quality greater than a specified value.
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
292
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
293 If the allele count equals the specified value (2) and the quality score for a SNP position is greater than the minimum quality score
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
294 value (150), the alternate allele is called.
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
295
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
296 However, if the allele count is 1, the position is called ambiguous. Deletions are called when the alternate allele is a gap. If the
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
297 quality score is less than or equal to the minimum quality score N value for alleles (150), the allele is marked "N".
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
298
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
299 **Required Options**
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
300
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
301 * **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.
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
302 * **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.
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
303
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
304 **Additional Options**
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
305
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
306 * **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).
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
307 * **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).
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
308 * **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).
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
309 * **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).
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
310 * **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.
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
311 * **Create a group containing all isolates?** - select Yes to output an additional group containing of all isolates.
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
312 </help>
3
14285a94fb13 Uploaded
greg
parents: 2
diff changeset
313 <expand macro="citations"/>
0
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
314 </tool>
ee4ef1fc23c6 Uploaded
greg
parents:
diff changeset
315