Mercurial > repos > iuc > virheat

annotate virheat.xml @ 3:b5411b5e8259 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 8f495733edea9287f6392a893c9429fd16b1cb1d
author iuc
date Mon, 26 Aug 2024 18:10:25 +0000
parents 927e55d1aa97
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d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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1 <tool id="virheat" name="VirHEAT: visualize allele frequencies"
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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2 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
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3 profile="@PROFILE@">
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4 <description>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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5 from VCFs as a heatmap and map mutations to respective genes
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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6 </description>
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7 <macros>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="biotools"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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11 <expand macro="requirements"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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12 <expand macro="version"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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13 <command detect_errors="exit_code"><![CDATA[
3
b5411b5e8259 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 8f495733edea9287f6392a893c9429fd16b1cb1d
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14
0
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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15 mkdir -p ./output_dir &&
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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16 #set $outfile = 'tmp_output.' + str($advanced.output_type)
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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17 #set $output_dir = 'output_dir/'
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18 bash vcfs_to_dir.sh &&
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d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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19 virheat
3
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20 'vcfs_dir/'
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21 '$output_dir'
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22 --name '$outfile'
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23 -r '$ref_id'
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24 #if $genome_data.choice == 'length'
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25 -l $genome_data.genome_length
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26 #else
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27 -g '$genome_data.gff3_file'
1
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28 #if $genome_data.annotations
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29 -a
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30 #for $an in $genome_data.annotations
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31 '${an.ann}'
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32 #end for
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33 #end if
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d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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34 #end if
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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35 #if $varfreq
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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36 -t $varfreq
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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37 #end if
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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38 $delete
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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39 -n $delete_n
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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40 #if $zoom.choice == 'yes'
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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41 -z $zoom.zoom_start $zoom.zoom_stop
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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42 #end if
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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43 $sort
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44 --min-cov $min_cov
1
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45 #for $sc in $scores
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46 -s '${sc.scores_file}' '${sc.pos_col}' '${sc.score_col}'
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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47 #if $sc.score_name
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48 '${sc.score_name}'
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49 #else
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50 '${sc.scores_file.element_identifier}'
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51 #end if
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52 #end for
0
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53 ]]></command>
3
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54 <configfiles>
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55 <configfile filename="vcfs_to_dir.sh"><![CDATA[
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56 mkdir -p 'vcfs_dir/' &&
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57 #for $input_file in $sinputs
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58 #set $sample_id = $input_file.element_identifier.replace("'", '_').replace('/', '_')
b5411b5e8259 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 8f495733edea9287f6392a893c9429fd16b1cb1d
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59 #set $file_path = 'vcfs_dir/' + $sample_id
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60 #if not $file_path.endswith('.vcf'):
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61 #set $file_path = $file_path + '.vcf'
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62 #end if
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63 ln -s '$input_file' '$file_path' &&
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64 #end for
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65 echo "VCF files are placed in vcfs_dir/."
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66 ]]></configfile>
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67 </configfiles>
0
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68 <inputs>
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69 <param name="sinputs" type="data_collection" format="vcf" label="Variant lists data" help="Select at least two datasets (or a dataset collection) with variant lists. Datasets are expected to represent individual samples and dataset names will be used as sample identifiers." multiple="true" collection_type="list" />
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70 <conditional name="genome_data">
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71 <param name="choice" type="select"
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72 label="Data for genomic annotation">
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73 <option value="length">length of the genome</option>
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74 <option value="gff3">gff3 file</option>
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75 </param>
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76 <when value="length">
1
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77 <param name="genome_length" argument="-l" type="integer" min="0" value="0" label="Genome length"/>
0
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78 </when>
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79 <when value="gff3">
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80 <param name="gff3_file" argument="-g" type="data" format="gff3" label="GFF3 file" help="GFF3 file contains annotations for the genome and allows to display genes harboring a mutation. Ensure that the file follows the GFF3 specification."/>
1
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81 <repeat name="annotations" title="Annotations" help="Add annotations from the GFF3 file to display. If no annotations are added, 'gene' will be used by default.">
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82 <param name="ann" type="text" value="gene" optional="false" label="Annotation name"/>
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83 </repeat>
0
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84 </when>
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85 </conditional>
3
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86 <param name="ref_id" argument="-r" type="text" optional="false" label="Reference identifier" help="Specify the ref id and generate plots for vcf with multiple refs, e.g. segmented viruses."/>
0
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87 <param name="varfreq" argument="-t" type="float" min="0" max="1" value="0" optional="true" label="Variant Frequency Threshold" help="Only plot variants with an intrasample frequency above this threshold in at least one sample." />
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88 <param argument="--delete" type="boolean" truevalue="--delete" falsevalue="--no-delete" checked="true" label="Delete mutations that are present in all samples and their maximum frequency divergence is smaller than 0.5"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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parents:
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89 <param name="delete_n" argument="-n" type="integer" min="0" value="0" label="Do not show mutations that occur n times or less"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
parents:
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90 <conditional name="zoom">
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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91 <param name="choice" type="select" label="Restrict the plot to a specific genomic region">
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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92 <option value="yes">Yes</option>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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93 <option value="no">No</option>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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94 </param>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
parents:
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95 <when value="yes">
2
927e55d1aa97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit de04f7ce4bd660f85b6182d7567a3279339439f5
iuc
parents: 1
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96 <param name="zoom_start" type="integer" value="0" label="Start"/>
927e55d1aa97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit de04f7ce4bd660f85b6182d7567a3279339439f5
iuc
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97 <param name="zoom_stop" type="integer" value="0" label="End"/>
0
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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98 </when>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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99 <when value="no"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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100 </conditional>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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101 <param argument="--sort" type="boolean" truevalue="--sort" falsevalue="--no-sort" checked="false" label="Sort sample names alphanumerically"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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102 <param argument="--min-cov" type="integer" min="1" max="1000" value="20" label="Display mutations covered at least x time"/>
1
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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103 <repeat name="scores" title="Scores" help="Include visualizations of additional scores (e.g., MAVE scores for binding affinity, expression level, antibody escape, etc.) mapped to mutations on the heatmap.">
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
parents: 0
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104 <param name="scores_file" type="data" format="csv" optional="false" label="CSV file" help="CSV file containing scores"/>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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105 <param name="pos_col" type="select" label="Mutation position column" help="The name of the column in the CSV file that contains the mutation positions in classic notation (e.g., T430Y)">
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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parents: 0
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106 <options>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
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107 <filter type="data_meta" ref="scores_file" key="column_names"/>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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108 </options>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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109 </param>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
parents: 0
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110 <param name="score_col" type="select" label="Scores column" help="The name of the column in the CSV file that contains the scores">
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
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111 <options>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
parents: 0
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112 <filter type="data_meta" ref="scores_file" key="column_names"/>
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113 </options>
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114 </param>
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115 <param name="score_name" type="text" optional="true" label="Score name" help="A descriptive name for the score to be used as labels in the plot. If not specified, the CSV file name will be used as the label instead"/>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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116 </repeat>
0
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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117 <section name="advanced" title="Image Properties" expanded="true">
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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118 <param name="output_type" type="select" label="Plot output format" >
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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119 <option value="pdf" selected="true" >PDF</option>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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120 <option value="png" >PNG</option>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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121 <option value="svg">SVG</option>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
parents:
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122 <option value="tiff" >TIFF</option>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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123 <option value="bmp" >BMP</option>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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124 <option value="jpeg" >JPEG</option>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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125 </param>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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126 </section>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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127 </inputs>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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128 <outputs>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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129 <data name="outfile" format="pdf" from_work_dir="output_dir/tmp_output.*"
1
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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130 label="VirHEAT: Variant-Frequency Plot on ${on_string}: ${advanced.output_type}">
0
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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131 <change_format>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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132 <when input="advanced.output_type" value="svg" format="svg" />
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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133 <when input="advanced.output_type" value="png" format="png" />
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
parents:
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134 <when input="advanced.output_type" value="tiff" format="tiff" />
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
parents:
diff changeset
135 <when input="advanced.output_type" value="bmp" format="bmp" />
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
parents:
diff changeset
136 <when input="advanced.output_type" value="jpeg" format="jpg" />
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
parents:
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137 </change_format>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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138 </data>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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diff changeset
139 </outputs>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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140 <tests>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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141 <test expect_num_outputs="1">
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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142 <!-- test1: gff3, pdf -->
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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143 <param name="sinputs" value="day_0.vcf,day_2.vcf,day_4.vcf,day_18.vcf,day_26.vcf,day_32.vcf,day_47.vcf,day_55.vcf,day_60.vcf,day_76.vcf,day_83.vcf,day_85.vcf,day_91.vcf,day_96.vcf,day_100.vcf,day_103.vcf,day_111.vcf"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
parents:
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144 <conditional name="genome_data">
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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145 <param name="choice" value="gff3"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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146 <param name="gff3_file" value="SARS-CoV-2.gff3"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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147 </conditional>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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148 <conditional name="zoom">
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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149 <param name="choice" value="yes"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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150 <param name="zoom_start" value="22599"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
parents:
diff changeset
151 <param name="zoom_stop" value="23278"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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152 </conditional>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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153 <output name="outfile" ftype="pdf">
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iuc
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154 <assert_contents>
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iuc
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155 <has_text text="day"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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156 </assert_contents>
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iuc
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157 </output>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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158 </test>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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159 <test expect_num_outputs="1">
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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160 <!-- test2: length, svg -->
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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diff changeset
161 <param name="sinputs" value="day_76.vcf,day_83.vcf,day_91.vcf,day_103.vcf" ftype="vcf" />
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
parents:
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162 <conditional name="genome_data">
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
parents:
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163 <param name="choice" value="length"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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164 <param name="genome_length" value="29903"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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165 </conditional>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
parents:
diff changeset
166 <conditional name="zoom">
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
parents:
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167 <param name="choice" value="yes"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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168 <param name="zoom_start" value="22599"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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169 <param name="zoom_stop" value="23278"/>
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170 </conditional>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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171 <output name="outfile" ftype="svg">
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172 <assert_contents>
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iuc
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173 <has_text text="day"/>
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174 </assert_contents>
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175 </output>
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iuc
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176 </test>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
parents:
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177 <test expect_num_outputs="1">
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178 <!-- test3: gff3, threshold, png, delete, delete-n -->
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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179 <param name="sinputs" value="day_76.vcf,day_83.vcf,day_91.vcf,day_103.vcf" ftype="vcf" />
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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180 <param name="varfreq" value="0.1"/>
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iuc
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181 <param name="delete" value="yes"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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182 <param name="delete_n" value="1"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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183 <conditional name="genome_data">
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iuc
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184 <param name="choice" value="gff3"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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185 <param name="gff3_file" value="SARS-CoV-2.gff3"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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186 </conditional>
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iuc
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187 <conditional name="zoom">
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188 <param name="choice" value="no"/>
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189 </conditional>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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190 <output name="outfile" ftype="png">
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191 <assert_contents>
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iuc
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192 <has_text text="day"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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193 </assert_contents>
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194 </output>
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195 </test>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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196 <test expect_num_outputs="1">
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197 <!-- test4: length, zoom, sort, tiff -->
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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198 <param name="sinputs" value="day_0.vcf,day_2.vcf,day_4.vcf,day_18.vcf,day_26.vcf,day_32.vcf,day_47.vcf,day_55.vcf,day_60.vcf,day_76.vcf,day_83.vcf,day_85.vcf,day_91.vcf,day_96.vcf,day_100.vcf,day_103.vcf,day_111.vcf"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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199 <param name="varfreq" value="0.1"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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200 <param name="delete" value="false"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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201 <param name="delete_n" value="0"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
parents:
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202 <param name="sort" value="true"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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203 <param name="min_cov" value="25"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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204 <conditional name="zoom">
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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205 <param name="choice" value="yes"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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206 <param name="zoom_start" value="22599"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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207 <param name="zoom_stop" value="23278"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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208 </conditional>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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209 <section name="advanced">
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iuc
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210 <param name="output_type" value="tiff"/>
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211 </section>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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212 <conditional name="genome_data">
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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213 <param name="choice" value="length"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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214 <param name="genome_length" value="29903"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
iuc
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215 </conditional>
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iuc
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216 <output name="outfile">
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iuc
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217 <assert_contents>
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iuc
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218 <has_text text="day"/>
d2a1ac520392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
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219 </assert_contents>
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220 </output>
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221 </test>
1
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
parents: 0
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222 <test expect_num_outputs="1">
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
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223 <!-- test5: annotations -->
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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224 <param name="sinputs" value="day_0.vcf,day_2.vcf,day_4.vcf,day_18.vcf,day_26.vcf,day_32.vcf,day_47.vcf,day_55.vcf,day_60.vcf,day_76.vcf,day_83.vcf,day_85.vcf,day_91.vcf,day_96.vcf,day_100.vcf,day_103.vcf,day_111.vcf"/>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
parents: 0
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225 <conditional name="genome_data">
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
parents: 0
diff changeset
226 <param name="choice" value="gff3"/>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
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227 <param name="gff3_file" value="SARS-CoV-2.gff3"/>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
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228 <repeat name="annotations">
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iuc
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229 <param name="ann" value="gene"/>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
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230 </repeat>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
parents: 0
diff changeset
231 <repeat name="annotations">
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iuc
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232 <param name="ann" value="CDS"/>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
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233 </repeat>
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234 </conditional>
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iuc
parents: 0
diff changeset
235 <conditional name="zoom">
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iuc
parents: 0
diff changeset
236 <param name="choice" value="yes"/>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
parents: 0
diff changeset
237 <param name="zoom_start" value="22599"/>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
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238 <param name="zoom_stop" value="23278"/>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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239 </conditional>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
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240 <output name="outfile" ftype="pdf">
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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241 <assert_contents>
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iuc
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242 <has_text text="day"/>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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243 </assert_contents>
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244 </output>
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iuc
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245 </test>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
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246 <test expect_num_outputs="1">
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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247 <!-- test6: scores -->
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248 <param name="sinputs" value="day_0.vcf,day_2.vcf,day_4.vcf,day_18.vcf,day_26.vcf,day_32.vcf,day_47.vcf,day_55.vcf,day_60.vcf,day_76.vcf,day_83.vcf,day_85.vcf,day_91.vcf,day_96.vcf,day_100.vcf,day_103.vcf,day_111.vcf"/>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
parents: 0
diff changeset
249 <conditional name="genome_data">
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
parents: 0
diff changeset
250 <param name="choice" value="gff3"/>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
parents: 0
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251 <param name="gff3_file" value="SARS-CoV-2.gff3"/>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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252 </conditional>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
parents: 0
diff changeset
253 <conditional name="zoom">
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iuc
parents: 0
diff changeset
254 <param name="choice" value="yes"/>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
parents: 0
diff changeset
255 <param name="zoom_start" value="22599"/>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
parents: 0
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256 <param name="zoom_stop" value="23278"/>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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257 </conditional>
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258 <repeat name="scores">
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iuc
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259 <param name="scores_file" value="MaveBindRBD.csv"/>
30584e80d61e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
iuc
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260 <param name="pos_col" value="AA"/>
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iuc
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261 <param name="score_col" value="score"/>
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262 <param name="score_name" value="binding"/>
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iuc
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263 </repeat>
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iuc
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264 <repeat name="scores">
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iuc
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265 <param name="scores_file" value="MaveExpRBD.csv"/>
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266 <param name="pos_col" value="AA"/>
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267 <param name="score_col" value="score"/>
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268 <param name="score_name" value="expression"/>
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269 </repeat>
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270 <output name="outfile" ftype="pdf">
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271 <assert_contents>
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272 <has_text text="day"/>
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273 </assert_contents>
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274 </output>
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275 </test>
0
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276 </tests>
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277 <help><![CDATA[
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278 @HELP_HEADER@
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279 ]]></help>
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280 <expand macro="citations"/>
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281 </tool>