Mercurial > repos > iuc > vsnp_build_tables

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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 06:11:08 +0000
parents 25714108bb22
children
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1 <tool id="vsnp_build_tables" name="vSNP: build tables" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description></description>
1
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <expand macro="biopython_requirement"/>
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8 <requirement type="package" version="0.25.3">pandas</requirement>
9
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9 <expand macro="xlsxwriter_requirement"/>
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10 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
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12 #import re
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13 #set output_excel_dir = 'output_excel_dir'
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14 #set input_type = $input_type_cond.input_type
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15 mkdir $output_excel_dir &&
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16 #if $input_type == "collection":
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17 #set input_newick_dir = 'input_newick_dir'
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18 mkdir $input_newick_dir &&
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19 #set input_json_avg_mq_dir = 'input_json_avg_mq_dir'
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20 mkdir $input_json_avg_mq_dir &&
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21 #set input_json_dir = 'input_json_dir'
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22 mkdir $input_json_dir &&
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23 #for $i in $input_type_cond.input_avg_mq_json_collection:
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24 #set file_name = $i.file_name
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25 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
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26 ln -s '$file_name' '$input_json_avg_mq_dir/$identifier' &&
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27 #end for
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28 #for $i in $input_type_cond.input_snps_json_collection:
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29 #set file_name = $i.file_name
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30 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
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31 ln -s '$file_name' '$input_json_dir/$identifier' &&
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32 #end for
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33 #for $i in $input_type_cond.input_newick_collection:
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34 #set file_name = $i.file_name
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35 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
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36 ln -s '$file_name' '$input_newick_dir/$identifier' &&
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37 #end for
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38 #end if
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39 python '$__tool_directory__/vsnp_build_tables.py'
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40 #if $input_type == "single":
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41 --input_avg_mq_json '$input_avg_mq_json'
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42 --input_snps_json '$input_snps_json'
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43 --input_newick '$input_newick'
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44 #end if:
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45 #if str($gbk_cond.gbk_param) == "yes":
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46 #set gbk_source_cond = $gbk_cond.gbk_source_cond
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47 #set gbk_source = $gbk_source_cond.gbk_source
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48 #if str($gbk_source) == "cached":
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49 --gbk_file '$gbk_source_cond.gbk_file.fields.path'
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50 #else:
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51 --gbk_file '$gbk_source_cond.gbk_file'
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52 #end if
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53 #end if
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54 --processes \${GALAXY_SLOTS:-8}
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55 ]]></command>
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56 <inputs>
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57 <conditional name="input_type_cond">
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58 <param name="input_type" type="select" label="Choose the category for the files to be analyzed">
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59 <option value="single" selected="true">Single files</option>
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60 <option value="collection">Collection of files</option>
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61 </param>
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62 <when value="single">
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63 <param name="input_snps_json" type="data" format="json" label="SNPs json file"/>
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64 <param name="input_avg_mq_json" type="data" format="json" label="Average MQ json file"/>
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65 <param name="input_newick" type="data" format="newick" label="Best-scoring ML tree file"/>
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66 </when>
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67 <when value="collection">
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68 <param name="input_snps_json_collection" format="json" type="data_collection" collection_type="list" label="Collection of SNPs json files"/>
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69 <param name="input_avg_mq_json_collection" format="json" type="data_collection" collection_type="list" label="Collection of average MQ json files"/>
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70 <param name="input_newick_collection" format="newick" type="data_collection" collection_type="list" label="Collection of best-scoring ML tree files"/>
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71 </when>
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72 </conditional>
0
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73 <conditional name="gbk_cond">
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74 <param name="gbk_param" type="select" label="Use Genbank file?">
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75 <option value="yes" selected="true">yes</option>
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76 <option value="no">No</option>
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77 </param>
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78 <when value="yes">
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79 <conditional name="gbk_source_cond">
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80 <param name="gbk_source" type="select" label="Choose the source for the Genbank file">
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81 <option value="cached" selected="true">locally cached</option>
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82 <option value="history">from history</option>
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83 </param>
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diff changeset
84 <when value="cached">
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
85 <param name="gbk_file" type="select" label="Genbank file">
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
86 <options from_data_table="vsnp_genbank">
4
efb86aade548 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2e312886647244b416c64eca91e1a61dd1be939b"
iuc
parents: 1
diff changeset
87 <validator type="no_options" message="A cached Genbank file is not available for the build associated with the selected average MQ json file"/>
0
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
88 </options>
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
89 </param>
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
90 </when>
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
91 <when value="history">
8
e54b96acea98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
parents: 6
diff changeset
92 <param name="gbk_file" type="data" format="genbank" label="Genbank file"/>
0
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
93 </when>
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
94 </conditional>
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
95 </when>
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
96 <when value="no"/>
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
97 </conditional>
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
98 </inputs>
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
99 <outputs>
9
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
100 <collection name="excel" type="list" format="xlsx" label="${tool.name} on ${on_string}">
4
efb86aade548 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2e312886647244b416c64eca91e1a61dd1be939b"
iuc
parents: 1
diff changeset
101 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;xlsx)" directory="output_excel_dir"/>
0
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
102 </collection>
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
103 </outputs>
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
104 <tests>
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
105 <test>
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
106 <param name="input_snps_json" value="input_snps_json.json" ftype="json" dbkey="89"/>
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
107 <param name="input_newick" value="input_newick.newick" ftype="newick" dbkey="89"/>
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
108 <param name="input_avg_mq_json" value="input_avg_mq_json.json" ftype="json" dbkey="89"/>
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
109 <param name="gbk_param" value="no"/>
4
efb86aade548 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2e312886647244b416c64eca91e1a61dd1be939b"
iuc
parents: 1
diff changeset
110 <output_collection name="excel" type="list" count="2">
9
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
111 <element name="cascade_table" ftype="xlsx">
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
112 <assert_contents>
11
6b3b0f5858e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
iuc
parents: 9
diff changeset
113 <has_size value="6766" delta="100"/>
9
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
114 </assert_contents>
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
115 </element>
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
116 <element name="sort_table" ftype="xlsx">
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
117 <assert_contents>
11
6b3b0f5858e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
iuc
parents: 9
diff changeset
118 <has_size value="6760" delta="100"/>
9
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
119 </assert_contents>
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
120 </element>
0
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
121 </output_collection>
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
122 </test>
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
123 <test>
9
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
124 <param name="input_type" value="collection"/>
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
125 <param name="input_snps_json_collection">
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
126 <collection type="list">
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
127 <element name="Mbovis-01_snps.json" value="Mbovis-01_snps.json" dbkey="89"/>
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
128 <element name="Mbovis-01D_snps.json" value="Mbovis-01D_snps.json" dbkey="89"/>
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
129 <element name="Mbovis-01D6_snps.json" value="Mbovis-01D6_snps.json" dbkey="89"/>
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
130 </collection>
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
131 </param>
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
132 <param name="input_newick_collection">
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
133 <collection type="list">
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
134 <element name="Mbovis-01_snps.newick" value="Mbovis-01_snps.newick" dbkey="89"/>
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
135 <element name="Mbovis-01D_snps.newick" value="Mbovis-01D_snps.newick" dbkey="89"/>
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
136 <element name="Mbovis-01D6_snps.newick" value="Mbovis-01D6_snps.newick" dbkey="89"/>
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
137 </collection>
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
138 </param>
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
139 <param name="input_avg_mq_json_collection">
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
140 <collection type="list">
11
6b3b0f5858e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
iuc
parents: 9
diff changeset
141 <element name="Mbovis-01_avg_mq.json" value="Mbovis-01_avg_mq.json" dbkey="89"/>
6b3b0f5858e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
iuc
parents: 9
diff changeset
142 <element name="Mbovis-01D_avg_mq.json" value="Mbovis-01D_avg_mq.json" dbkey="89"/>
6b3b0f5858e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
iuc
parents: 9
diff changeset
143 <element name="Mbovis-01D6_avg_mq.json" value="Mbovis-01D6_avg_mq.json" dbkey="89"/>
9
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
144 </collection>
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
145 </param>
0
5e258fba246c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
iuc
parents:
diff changeset
146 <param name="gbk_param" value="no"/>
9
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
147 <output_collection name="excel" type="list" count="6">
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
148 <element name="Mbovis-01D6_snps_cascade_table" ftype="xlsx">
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
149 <assert_contents>
11
6b3b0f5858e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
iuc
parents: 9
diff changeset
150 <has_size value="6767" delta="100"/>
9
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
151 </assert_contents>
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
152 </element>
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
153 <element name="Mbovis-01D6_snps_sort_table" ftype="xlsx">
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
154 <assert_contents>
11
6b3b0f5858e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
iuc
parents: 9
diff changeset
155 <has_size value="6761" delta="100"/>
9
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
156 </assert_contents>
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
157 </element>
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
158 <element name="Mbovis-01D_snps_cascade_table" ftype="xlsx">
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
159 <assert_contents>
11
6b3b0f5858e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
iuc
parents: 9
diff changeset
160 <has_size value="6767" delta="100"/>
9
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
161 </assert_contents>
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
162 </element>
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
163 <element name="Mbovis-01D_snps_sort_table" ftype="xlsx">
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
164 <assert_contents>
11
6b3b0f5858e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
iuc
parents: 9
diff changeset
165 <has_size value="6761" delta="100"/>
9
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
166 </assert_contents>
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
167 </element>
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
168 <element name="Mbovis-01_snps_cascade_table" ftype="xlsx">
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents: 8
diff changeset
169 <assert_contents>
11
6b3b0f5858e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
iuc
parents: 9
diff changeset
170 <has_size value="6767" delta="100"/>
9
25714108bb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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171 </assert_contents>
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172 </element>
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173 <element name="Mbovis-01_snps_sort_table" ftype="xlsx">
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174 <assert_contents>
11
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175 <has_size value="6761" delta="100"/>
9
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176 </assert_contents>
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177 </element>
0
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178 </output_collection>
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179 </test>
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180 </tests>
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181 <help>
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182 **What it does**
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183
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184 Accepts a combination of single SNPs json, average MQ json and newick files (or associated collections of
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185 each) to produce annotated SNPs tables in the form of Excel spreadsheets. The SNPs json and average MQ json
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186 files are typically produced by the **vSNP: get SNPs** tool and the newick files are typically produced by
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187 the **Phyogenetic reconstruction with RaXML** tool.
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188
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189 The SNPs tables display closely related isolates and enables identification of mixed SNPs when multiple
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190 bacterial strains are infecting an organism. The table structure is shown below. The columns identify the
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191 genome location of the SNP calls and the isolates are contained within the rows. The reference (or ancestral
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192 strain if the reference is an outgroup) is listed across the top, identified as the "reference call". SNPs
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193 that are not highlighted will match the reference. The map-quality row values are the average of the map
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194 quality scores of each isolate in that position. These scores measure the confidence that the read has been
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195 mapped to the correct location on the genome. The maximum score possible is 60, and lower scores lessen the
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196 confidence that the SNP was correctly identified. The annotation of the position is provided at the bottom
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197 of the table.
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198
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199 .. image:: table_description.png
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200
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201 SNPs are sorted according to their evolutionary age within the table. The oldest SNPs (encompassing the most
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202 isolates) are furthest to the left. This sorting is somewhat crude - the intent is to improve readibility or
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203 more easily match a related tree.
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204
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205 For a more detailed discussion, see the **Validating and correcting SNP calls** section of
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206 the `vSNP documentation`_.
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207
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208 .. _vSNP documentation: https://github.com/USDA-VS/vSNP/blob/master/docs/detailed_usage.md
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209
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210 **Required Options**
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211
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212 * **Choose the category for the files to be analyzed** - select "Single files" or "Collections of files", then select the appropriate history items (single SNPs json, average MQ json and newick files, or collections of each) based on the selected option.
0
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213 * **Use Genbank file** - Select "yes" to annotate the tables using the information in the Genbank file. Locally cached files, if available, provide the most widely used annotations, but more custom Genbank files can be chosen from the current history.
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214 </help>
1
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215 <expand macro="citations"/>
0
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216 </tool>
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217