Mercurial > repos > iuc > snpfreqplot

annotate snpfreqplot.xml @ 2:59a7bb93b5fe draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
author iuc
date Fri, 18 Dec 2020 23:47:31 +0000
parents 480821a403a0
children eaeb1b3dc23d
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469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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1 <tool id="snpfreqplot" name="Variant Frequency Plot" version="@VERSION@+galaxy@GALAXY_VERSION@" profile="20.09"
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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2 license="GPL-3.0-or-later" >
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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3 <description>Generates a heatmap of allele frequencies grouped by variant type for SnpEff-annotated SARS-CoV-2 data</description>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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4 <macros>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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5 <token name="@VERSION@">1.0</token>
2
59a7bb93b5fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
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6 <token name="@GALAXY_VERSION@">2</token>
0
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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7 </macros>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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8 <requirements>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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9 <requirement type="package" version="4.0">r-base</requirement>
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10 <requirement type="package" version="1.0.12">r-pheatmap</requirement>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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11 <requirement type="package" version="1.3.0">r-tidyverse</requirement>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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12 <requirement type="package" version="1.36.0">bioconductor-variantannotation</requirement>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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13 </requirements>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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14 <edam_topics>
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15 <edam_topic>topic_0797</edam_topic>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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16 <edam_topic>topic_0092</edam_topic>
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17 </edam_topics>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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18 <edam_operations>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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19 <edam_operation>operation_3436</edam_operation>
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20 </edam_operations>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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21 <command detect_errors="exit_code"><![CDATA[
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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22 #set $outfile = "tmp_output." + str($advanced.output_type)
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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23
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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24 cat '$__tool_directory__/helperFunctions.R' > /dev/null
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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25 && cat '$__tool_directory__/snpEffExtract.R' > /dev/null
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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26 && cat '$__tool_directory__/heatmap_for_variants.R' > /dev/null
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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27 && echo "output file: $outfile"
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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28 && Rscript '$configscript'
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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29 ]]>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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30 </command>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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31 <configfiles>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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32 <configfile name="configscript"><![CDATA[
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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33 ## 1. Set Sample Inputs
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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34 ## ------------------
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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35 ## Create a dataframe of sample ids, filetypes, and filenames
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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36 ## from the input collection. At this point, the list could be
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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37 ## of mixed type (vcf and tabular), though maybe Galaxy
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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38 ## restricts that.
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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39 samples = list(ids = c(), exts= c(), files = c())
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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40 #for $i, $file in enumerate($sinputs):
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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41 samples\$ids = c(samples\$ids, '${file.element_identifier}')
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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42 samples\$exts = c(samples\$exts, '${file.extension}')
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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43 samples\$files = c(samples\$files, '${file}')
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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44 #end for
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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45 samples = data.frame(samples, stringsAsFactors=F)
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46
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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47 ## 2. Input Conversion (external script)
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48 ## ----------------------------------
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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49 ## We source the input conversion script *after* the samples
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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50 ## have been populated, so that it performs an inplace replacement
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51 ## of the vcf inputs with their converted tabular counterparts.
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52 ##
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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53 ## All samples are all tabular after this point
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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54 source('$__tool_directory__/helperFunctions.R')
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55 source('$__tool_directory__/snpEffExtract.R')
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56
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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57 ## 3. Galaxy Params
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58 ## --------------
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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59 ## Set the general script parameters from the UI
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60 variant_frequency <- as.numeric( '$varfreq' )
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61 brewer_color_gene_annotation <- as.character( '$advanced.color' )
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62
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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63 #if str($clustering.do) == "TRUE":
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64 pheat_clustering <- TRUE
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65 pheat_clustering_method <- as.character( '$clustering.method' )
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66 pheat_number_of_clusters <- as.integer( '$clustering.nclust' )
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67 #else
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68 pheat_clustering <- FALSE
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69 pheat_clustering_method <- "ward.D2"
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70 pheat_number_of_clusters <- 5
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71 #end if
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72
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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73 ratio = as.numeric('$advanced.ratio')
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74 out_ext = '$advanced.output_type'
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75 out_file = paste0("tmp_output.", out_ext)
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76
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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77 ## 4. Generate Heatmap (external script)
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78 ## ----------------------------------
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79 source('$__tool_directory__/heatmap_for_variants.R')
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80
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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81 ]]>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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82 </configfile>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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83 </configfiles>
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84 <inputs>
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85 <param name="sinputs" format="tabular,vcf" type="data" multiple="true"
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parents:
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86 collection_type="list" label="Variant lists data"
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
87 help="Select at least two datasets (or a dataset collection) with variant lists (see the tool help below for format details). Datasets are expected to represent individual samples and dataset names will be used as sample identifiers." />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
88 <param name="varfreq" type="float" min="0" max="1" value="0.1"
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
89 label="Variant Frequency Threshold"
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
90 help="Only plot variants with an intrasample frequency above this threshold in at least one sample." />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
91 <section name="advanced" title="Image Properties" expanded="true">
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
92 <param name="output_type" type="select" label="Plot output format" >
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
93 <option value="pdf" selected="true" >PDF</option>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
94 <option value="png" >PNG</option>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
95 <option value="svg">SVG</option>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
96 <option value="tiff" >TIFF</option>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
97 <option value="bmp" >BMP</option>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
98 <option value="jpeg" >JPEG</option>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
99 </param>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
100 <param name="ratio" label="Cell Ratio" type="float"
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
101 min="0.05" value="0.67" max="20"
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
102 help="Width:Height ratio of individual heatmap cells" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
103 <param name="color" type="select" label="Color palette used for the gene annotations" >
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
104 <option value="Set1" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
105 <option value="Set2" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
106 <option value="Set3" selected="true" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
107 <option value="Pastel2" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
108 <option value="Pastel1" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
109 <option value="Paired" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
110 <option value="Dark2" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
111 <option value="Accent" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
112 <option value="YlOrRd" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
113 <option value="YlOrBr" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
114 <option value="YlGnBu" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
115 <option value="YlGn" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
116 <option value="Reds" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
117 <option value="RdPu" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
118 <option value="Purples" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
119 <option value="PuRd" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
120 <option value="PuBuGn" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
121 <option value="PuBu" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
122 <option value="OrRd" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
123 <option value="Oranges" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
124 <option value="Greys" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
125 <option value="Greens" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
126 <option value="GnBu" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
127 <option value="BuPu" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
128 <option value="BuGn" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
129 <option value="Blues" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
130 <option value="Spectral" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
131 <option value="RdYlGn" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
132 <option value="RdYlBu" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
133 <option value="RdGy" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
134 <option value="RdBu" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
135 <option value="PuOr" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
136 <option value="PRGn" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
137 <option value="PiYG" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
138 <option value="BrBG" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
139 </param>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
140 </section>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
141 <conditional name="clustering">
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
142 <param name="do" type="select" label="Perform Clustering?" >
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
143 <option value="TRUE">Yes</option>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
144 <option value="FALSE" selected="true">No</option>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
145 </param>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
146 <when value="TRUE" >
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
147 <param name="nclust" type="integer"
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
148 min="1" value="1" label="Number of clusters" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
149 <param name="method" type="select" label="Clustering method" >
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
150 <option value="ward.D" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
151 <option value="ward.D2" selected="true" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
152 <option value="single" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
153 <option value="complete" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
154 <option value="average" >average (UPGMA)</option>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
155 <option value="mcquitty" >mcquitty (WPGMA)</option>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
156 <option value="median" >median (WPGMC)</option>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
157 <option value="centroid" >centroid (UPGMC)</option>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
158 </param>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
159 </when>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
160 <when value="FALSE" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
161 </conditional>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
162 </inputs>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
163 <outputs>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
164 <data name="outfile" format="pdf" from_work_dir="tmp_output.*"
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
165 label="Variant-Frequency Plot on ${on_string}: ${advanced.output_type}">
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
166 <change_format>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
167 <when input="advanced.output_type" value="svg" format="svg" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
168 <when input="advanced.output_type" value="png" format="png" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
169 <when input="advanced.output_type" value="tiff" format="tiff" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
170 <when input="advanced.output_type" value="bmp" format="bmp" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
171 <when input="advanced.output_type" value="jpeg" format="jpg" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
172 </change_format>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
173 </data>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
174 </outputs>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
175 <tests>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
176 <test expect_num_outputs="1">
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
177 <!-- PDF, tabular inputs -->
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
178 <param name="sinputs" ftype="tabular" value="input436.tabular,input437.tabular,input438.tabular,input439.tabular,input440.tabular,input441.tabular,input442.tabular,input443.tabular,input444.tabular" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
179 <output name="outfile" ftype="pdf" value="heatmap.default.pdf" compare="sim_size" delta="250" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
180 </test>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
181 <test expect_num_outputs="1">
2
59a7bb93b5fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
iuc
parents: 1
diff changeset
182 <!-- PDF, tabular inputs, short color palette -->
59a7bb93b5fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
iuc
parents: 1
diff changeset
183 <param name="sinputs" ftype="tabular" value="input436.tabular,input437.tabular,input438.tabular,input439.tabular,input440.tabular,input441.tabular,input442.tabular,input443.tabular,input444.tabular" />
59a7bb93b5fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
iuc
parents: 1
diff changeset
184 <section name="advanced" >
59a7bb93b5fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
iuc
parents: 1
diff changeset
185 <param name="color" value="Set2" />
59a7bb93b5fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
iuc
parents: 1
diff changeset
186 </section>
59a7bb93b5fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
iuc
parents: 1
diff changeset
187 <output name="outfile" ftype="pdf" value="heatmap.default.pdf" compare="sim_size" delta="250" />
59a7bb93b5fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
iuc
parents: 1
diff changeset
188 </test>
59a7bb93b5fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
iuc
parents: 1
diff changeset
189 <test expect_num_outputs="1">
0
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
190 <!-- PNG, multiple inputs, non-numeric IDS -->
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
191 <param name="sinputs" ftype="tabular" value="input436.tabular,input437.tabular,input443.tabular,input444.tabular" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
192 <param name="varfreq" value="0.5" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
193 <section name="advanced" >
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
194 <param name="color" value="Spectral" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
195 <param name="output_type" value="png" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
196 </section>
1
480821a403a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1bde09fccd1a5412240ebd5c1f34a45ad73cebe2"
iuc
parents: 0
diff changeset
197 <output name="outfile" ftype="png" value="heatmap.imageopts.png" compare="sim_size" delta="100000" />
0
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
198 </test>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
199 <test expect_num_outputs="1">
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
200 <!-- SVG, clustering defaults -->
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
201 <param name="sinputs" ftype="tabular" value="input438.tabular,input439.tabular,input440.tabular,input441.tabular,input442.tabular" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
202 <conditional name="clustering">
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
203 <param name="do" value="TRUE" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
204 </conditional>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
205 <section name="advanced" >
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
206 <param name="color" value="Greys" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
207 <param name="ratio" value="0.8" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
208 <param name="output_type" value="svg" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
209 </section>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
210 <output name="outfile" ftype="svg">
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
211 <assert_contents>
1
480821a403a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1bde09fccd1a5412240ebd5c1f34a45ad73cebe2"
iuc
parents: 0
diff changeset
212 <has_text text="viewBox=&quot;0 0 1156 361&quot;" />
0
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
213 </assert_contents>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
214 </output>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
215 </test>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
216 <test expect_num_outputs="1">
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
217 <!-- JPEG, clustering extras, mixed alphanumeric labels -->
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
218 <param name="sinputs" ftype="tabular" value="input436.tabular,input443.tabular,input438.tabular,input444.tabular" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
219 <conditional name="clustering">
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
220 <param name="do" value="TRUE" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
221 <param name="nclust" value="2" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
222 <param name="method" value="centroid" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
223 </conditional>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
224 <section name="advanced" >
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
225 <param name="color" value="Purples" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
226 <param name="ratio" value="1.2" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
227 <param name="output_type" value="jpeg" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
228 </section>
1
480821a403a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1bde09fccd1a5412240ebd5c1f34a45ad73cebe2"
iuc
parents: 0
diff changeset
229 <output name="outfile" ftype="jpg" value="heatmap.clustering2.jpeg" compare="sim_size" delta="130000" />
0
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
230 </test>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
231 <test expect_num_outputs="1">
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
232 <!-- PDF, vcf test -->
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
233 <param name="sinputs" ftype="vcf" value="snpeff.123.vcf,snpeff.456.vcf,snpeff.789.vcf" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
234 <section name="advanced" >
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
235 <param name="color" value="PuBuGn" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
236 <param name="output_type" value="pdf" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
237 </section>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
238 <output name="outfile" ftype="pdf" value="heatmap.from_vcf.pdf" compare="sim_size" delta="250" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
239 </test>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
240 <test expect_num_outputs="1">
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
241 <!-- SVG, problematic vcf test -->
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
242 <param name="sinputs" ftype="vcf" value="1084592.vcf,1085080.vcf,1085445.vcf,1085841.vcf,1085990.vcf" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
243 <section name="advanced" >
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
244 <param name="output_type" value="svg" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
245 </section>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
246 <output name="outfile" ftype="svg">
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
247 <assert_contents>
1
480821a403a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1bde09fccd1a5412240ebd5c1f34a45ad73cebe2"
iuc
parents: 0
diff changeset
248 <has_text text="viewBox=&quot;0 0 754 292&quot;" />
0
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
249 </assert_contents>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
250 </output>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
251 </test>
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
252 <test expect_num_outputs="1">
2
59a7bb93b5fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
iuc
parents: 1
diff changeset
253 <!-- SVG, Vcf test with problematic splice+syn at snpeff789.vcf for threshold = 0.0222
59a7bb93b5fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
iuc
parents: 1
diff changeset
254 and an "empty" file (no variants) and a file with just one variant among its inputs -->
59a7bb93b5fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
iuc
parents: 1
diff changeset
255 <param name="sinputs" ftype="vcf" value="snpeff.123.vcf,snpeff.456.vcf,snpeff.789.vcf,no_variants.vcf,single_variant.vcf" />
0
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
256 <param name="varfreq" value="0.0222" />
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
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257 <section name="advanced" >
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258 <param name="output_type" value="svg" />
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259 </section>
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260 <output name="outfile" ftype="svg">
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261 <assert_contents>
2
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262 <has_text text="viewBox=&quot;0 0 1962 546&quot;" />
0
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263 </assert_contents>
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264 </output>
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265 </test>
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266 </tests>
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267 <help><![CDATA[
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268 **What it does**
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269
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270 This tool generates multi-sample variant-frequency plots from SnpEff-annotated
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271 viral variant lists with optional hierarchical clustering of the samples.
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272
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273 .. class:: Warning mark
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274
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275 Currently, this tool has been tested only on SARS-CoV-2 variant data.
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276 While the intention is to have it work for viral variant data in general,
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277 be prepared for unexpected behavior with other input data at the current
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278 development stage.
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279
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280 ----
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281
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282 The tool expects input variant lists in one of the following two formats:
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283
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284 1. VCF datasets as produced by standard variant callers with
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285
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286 - variant allele frequencies encoded in an ``AF`` INFO field
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287 - variant functional genomic effects annotated using SnpEff's EFF format (SnpEff's ANN format is not currently supported!)
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288
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289 2. tabular datasets with columns listing, at least, the following variant properties:
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290
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291 - ``CHROM``
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292 - ``POS``
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293 - ``REF``
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294 - ``ALT``
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295 - ``AF``
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296 - ``EFF[*].AA``
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297 - ``EFF[*].GENE``
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298 - ``EFF[*].EFFECT``
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299
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300 Such files can be produced with SnpSift Extract Fields and can be useful if
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301 preprocessing of the lists with standard text processing tools is required.
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302
1
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303 .. class:: infomark
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304
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305 To represent empty EFF fields in the tabular format you can choose between
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306 ``.`` and the empty string.
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307
0
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308 ----
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309
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310 Example output:
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311
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312 .. image:: /static/images/example_output.png
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313
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314 ]]></help>
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315 <citations>
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316 <citation type="bibtex">@unpublished{Fuchs2020,
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317 author = {Fuchs, Jonas},
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318 title = {},
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319 year = {2020},
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320 note = {Multi-sample annotated viral variant-frequency plots based on the R pheatmap package.},
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321 address = {Institute for Virology, University of Freiburg}
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322 }</citation>
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323 </citations>
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324 </tool>