Mercurial > repos > iuc > coverm_genome

annotate coverm_genome.xml @ 4:c4e3aa19841c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit bc3831e3648809bd3d46611b2a74bd26a17985e5
author iuc
date Fri, 18 Aug 2023 09:22:54 +0000
parents dd96e74908a9
children
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b6a241c73012 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2388df7187533fb66b7729730340d2eb7b93c112
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1 <tool id="coverm_genome" name="CoverM genome" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
b6a241c73012 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2388df7187533fb66b7729730340d2eb7b93c112
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2 <description>Calculate coverage of individual genomes</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
3
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <command><![CDATA[
3
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9 #import re
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10
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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11 #set $single_fp = []
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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12 #set $fw_fp = []
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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13 #set $rv_fp = []
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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14 #set $interl_fp = []
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15 #set $ref_fp = []
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16 #set $bam_fp = []
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17 #set $genome_fp = []
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18
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19 mkdir 'single/' &&
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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20 mkdir 'fw/' &&
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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21 mkdir 'rv/' &&
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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22 mkdir 'interl/' &&
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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23 mkdir 'ref/' &&
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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24 mkdir 'bam/' &&
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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25
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26 #if $mapped.mapped == 'mapped'
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27 @BAMS@
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28 #if $mapped.genome.ref_or_genome == 'genomic'
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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29 #if $mapped.genome.genomic.source == 'history'
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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30 #for $i, $genome in enumerate($mapped.genome.genomic.genome_fasta_files)
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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31 #set $fn = re.sub('[^\s\w\-\\.]', '_', str($genome.element_identifier))
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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32 #silent $genome_fp.append( $fn )
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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33 ln -s '$genome' '$fn' &&
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34 #end for
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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35 #else
3
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36 #for $i, $genome in enumerate($mapped.genome.genomic.genome_fasta_files)
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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37 #set $fn = re.sub('[^\s\w\-\\.]', '_', str($genome.fields.path.element_identifier))
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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38 #silent $genome_fp.append( $fn )
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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39 ln -s '$genome' '$fn' &&
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40 #end for
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41 #end if
3
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42 #end if
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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43 #else
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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44 #if $mapped.mode.mode == 'individual'
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45 @INDIVIDUAL_ASSEMBLY_READS@
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46 #if $mapped.mode.genome.ref_or_genome == 'genomic'
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47 @GENOME_FOR_READS@
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48 #else
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49 #set $ref = $mapped.mode.genome.reference
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50 @INDIVIDUAL_ASSEMBLY_REF@
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51 #end if
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52 #else
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53 @CO_ASSEMBLY_ALL_READS@
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54 #if $mapped.mode.genome.ref_or_genome == 'genomic'
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55 @GENOME_FOR_READS@
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56 #else
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57 #set $refs = $mapped.mode.genome.reference
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58 @CO_ASSEMBLY_REF@
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59 #end if
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60 #end if
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61 #end if
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62
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63 mkdir 'representative-fasta/' &&
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64 coverm
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65 genome
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66 #if $mapped.mapped == 'mapped'
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67 -b
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68 #for $bam in $bam_fp
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69 '$bam'
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70 #end for
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71 #if $mapped.genome.ref_or_genome == 'contigs'
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72 $mapped.genome.cond_single_genome.single_genome
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73 #if $mapped.genome.cond_single_genome.single_genome == ''
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74 #if $mapped.genome.cond_single_genome.genome_contig_definition.choice == 'genome-definition'
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75 --genome-definition '$mapped.genome.cond_single_genome.genome_contig_definition.genome_definition'
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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76 #else if $mapped.genome.cond_single_genome.genome_contig_definition.choice == 'separator'
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77 --separator '$mapped.genome.cond_single_genome.genome_contig_definition.separator'
0
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78 #end if
3
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79 #end if
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80 $mapped.sharded
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81 #else
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82 --genome-fasta-files
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83 #for $genome in $genome_fp
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84 '$genome'
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85 #end for
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86 #end if
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87 #else
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88 #if $fw_fp
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89 -1
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90 #for $read in $fw_fp
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91 '$read'
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92 #end for
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93 -2
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94 #for $read in $rv_fp
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95 '$read'
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96 #end for
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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97 #else if $single_fp
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98 --single
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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99 #for $read in $single_fp
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100 '$read'
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101 #end for
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102 #else if $interl_fp
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103 --interleaved
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104 #for $read in $interl_fp
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105 '$read'
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106 #end for
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107 #end if
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108
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109 --mapper '$mapped.mapper'
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110 #if $mapped.mode.genome.ref_or_genome == 'contigs'
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111 --reference
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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112 #for $ref in $ref_fp
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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113 '$ref'
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114 #end for
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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115 $mapped.mode.genome.cond_single_genome.single_genome
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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116 #if $mapped.mode.genome.cond_single_genome.single_genome == ''
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117 #if $mapped.mode.genome.cond_single_genome.genome_contig_definition.choice == 'genome-definition'
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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118 --genome-definition '$mapped.mode.genome.cond_single_genome.genome_contig_definition.genome_definition'
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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119 #else if $mapped.mode.genome.cond_single_genome.genome_contig_definition.choice == 'separator'
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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120 --separator '$mapped.mode.genome.cond_single_genome.genome_contig_definition.separator'
0
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121 #end if
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122 #end if
3
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123 #if $mapped.mode.mode == 'co'
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124 $mapped.mode.genome.sharded
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125 #end if
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126 #else
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127 --genome-fasta-files
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128 #for $genome in $genome_fp
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129 '$genome'
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130 #end for
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131 #end if
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132 #end if
0
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133
3
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134 $exclude_genomes_from_deshard
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135 --min-read-aligned-length $alignment.min_read_aligned_length
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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136 --min-read-percent-identity $alignment.min_read_percent_identity
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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137 --min-read-aligned-percent $alignment.min_read_aligned_percent
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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138 $alignment.proper_pairs_only.proper_pairs_only
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139 #if $alignment.proper_pairs_only.proper_pairs_only != ''
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140 --min-read-aligned-length-pair $alignment.proper_pairs_only.min_read_aligned_length_pair
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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141 --min-read-percent-identity-pair $alignment.proper_pairs_only.min_read_percent_identity_pair
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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142 --min-read-aligned-percent-pair $alignment.proper_pairs_only.min_read_aligned_percent_pair
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143 #end if
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144
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145 --methods
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146 #for method in $cov.methods
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147 '$method'
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148 #end for
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149 --min-covered-fraction $cov.min_covered_fraction
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150 --contig-end-exclusion $cov.contig_end_exclusion
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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151 --trim-min $cov.trim_min
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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152 --trim-max $cov.trim_max
0
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153
3
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154 $derep.dereplicate.dereplicate
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155 #if $derep.dereplicate.dereplicate != ''
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156 --dereplication-ani $derep.dereplicate.dereplication_ani
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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157 --dereplication-aligned-fraction $derep.dereplicate.dereplication_aligned_fraction
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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158 --dereplication-fragment-length $derep.dereplicate.dereplication_fragment_length
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159 --dereplication-prethreshold-ani $derep.dereplicate.dereplication_prethreshold_ani
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160 --dereplication-quality-formula '$derep.dereplicate.dereplication_quality_formula'
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161 --dereplication-precluster-method '$derep.dereplicate.dereplication_precluster_method'
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162 #end if
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163 #if $derep.checkm_tab_table
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164 --chekm-tab-table '$derep.checkm_tab_table'
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165 #end if
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166 #if $derep.genome_info:
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167 --genome-info '$derep.genome_info'
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168 #end if
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169 #if $derep.min_completeness != "":
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170 --min-completeness $derep.min_completeness
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171 #end if
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172 #if $derep.max_contamination != "":
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173 --max-contamination $derep.max_contamination
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174 #end if
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175
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176 --output-format '$out.output_format'
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177 --output-file '$output'
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178 $out.no_zeros
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179 #if $out.dereplication_output_cluster_definition:
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180 --dereplication-output-cluster-definition '$cluster_definition'
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181 #end if
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182 #if $out.dereplication_output_representative_fasta_directory_copy:
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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183 --dereplication-output-representative-fasta-directory-copy './representative-fasta/'
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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184 #end if
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185 --threads \${GALAXY_SLOTS:-1}
0
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186
3
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187 #if $derep.dereplicate.dereplicate and $out.dereplication_output_cluster_definition
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188 && sed -i -e 's@genomes/@@g; s/\.fna//g' '$cluster_definition'
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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189 #end if
0
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190 ]]></command>
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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191 <inputs>
3
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192 <conditional name="mapped">
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193 <expand macro="mapped"/>
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194 <when value="mapped">
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195 <expand macro="mapped_params"/>
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196 <conditional name="genome">
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197 <param name="ref_or_genome" type="select" label="Genome definition">
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198 <option value="contigs" selected="true">From contigs in the BAM file(s)</option>
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199 <option value="genomic">From FASTA files with each genome</option>
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200 </param>
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201 <when value="contigs">
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202 <expand macro="cond_single_genome"/>
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203 </when>
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204 <when value="genomic">
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205 <expand macro="genomic"/>
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206 </when>
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207 </conditional>
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208 </when>
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209 <when value="not-mapped">
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210 <conditional name="mode">
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211 <expand macro="assembly_mode"/>
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212 <when value="individual">
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213 <expand macro="individual_assembly_reads"/>
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214 <conditional name="genome">
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215 <expand macro="ref_or_genome"/>
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216 <when value="contigs">
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217 <expand macro="individual_assembly_reference"/>
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218 <expand macro="cond_single_genome"/>
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219 </when>
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220 <when value="genomic">
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221 <expand macro="genomic"/>
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222 </when>
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223 </conditional>
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224 </when>
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225 <when value="co">
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226 <expand macro="co_assembly_reads"/>
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227 <repeat name="extra_reads" title="Additional reads">
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228 <expand macro="co_assembly_reads"/>
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229 </repeat>
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230 <conditional name="genome">
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231 <expand macro="ref_or_genome"/>
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232 <when value="contigs">
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233 <expand macro="co_assembly_reference"/>
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234 <expand macro="cond_single_genome"/>
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235 </when>
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236 <when value="genomic">
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237 <expand macro="genomic"/>
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238 </when>
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239 </conditional>
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240 </when>
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241 </conditional>
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242 <expand macro="mapping"/>
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243 </when>
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244 </conditional>
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245 <param argument="--exclude-genomes-from-deshard" type="boolean" truevalue="--exclude-genomes-from-deshard" falsevalue="" checked="false" label="Exclude genomes from deshard"
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246 help="Ignore genomes whose name appears in this newline-separated file when combining shards." />
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247 <expand macro="alignment"/>
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248 <section name="cov" title="Coverage calculation options" expanded="false">
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249 <param argument="--methods" type="select" multiple="true" label="Method(s) for calculating coverage">
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250 <option value="relative_abundance" selected="true">relative_abundance: Percentage relative abundance of each genome, and the unmapped read percentage</option>
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251 <option value="mean">mean: Average number of aligned reads overlapping each position on the contig</option>
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252 <expand macro="cov_method_options"/>
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253 </param>
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254 <expand macro="coverage_params"/>
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255 </section>
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256 <section name="derep" title="Dereplication / Genome clustering" expanded="false">
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257 <conditional name="dereplicate">
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258 <param argument="--dereplicate" type="select" label="Do genome dereplication via average nucleotide identity (ANI)?" help="When this is run,
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259 dereplication occurs transparently through the Galah method.">
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260 <option value="--dereplicate">Yes</option>
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261 <option value="" selected="false">No</option>
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262 </param>
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263 <when value="--dereplicate">
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264 <param argument="--dereplication-ani" type="float" min="0" max="100" value="99" label="Overall ANI level to dereplicate at with FastANI" />
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265 <param argument="--dereplication-aligned-fraction" type="float" min="0" value="50" label="Minimum aligned fraction of two genomes for clustering" />
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266 <param argument="--dereplication-fragment-length" type="integer" min="0" value="3000" label="Length of fragment used in FastANI calculation (i.e. --fragLen)" />
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267 <param argument="--dereplication-quality-formula" type="select" label="Scoring function for genome quality">
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268 <option value="Parks2020_reduced" selected="true">Parks2020_reduced: A quality formula described in Parks et. al. 2020</option>
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269 <option value="completeness-4contamination">completeness-4contamination</option>
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270 <option value="completeness-5contamination">completeness-5contamination</option>
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271 <option value="dRep">dRep</option>
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272 </param>
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273 <param argument="--dereplication-prethreshold-ani" type="float" min="0" max="100" value="95" label="Dereplication preclustering threshold"
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274 help="Require at least this dashing-derived ANI for preclustering and to avoid FastANI on distant lineages within preclusters." />
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275 <param argument="--dereplication-precluster-method" type="select" label="Method of calculating rough ANI for dereplication">
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276 <option value="dashing" selected="true">dashing: HyperLogLog</option>
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277 <option value="finch">finch: finch MinHash</option>
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278 </param>
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279 </when>
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280 <when value=""/>
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281 </conditional>
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282 <param argument="--checkm-tab-table" type="data" format="tabular" optional="true" label="checkM table for defining genome quality"
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283 help="It is used both for filtering and to rank genomes during clustering"/>
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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284 <param argument="--genome-info" type="data" format="csv" optional="true"
3
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285 label="dRep style genome info table for defining quality" />
0
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286 <param argument="--min-completeness" type="float" optional="true" min="0" max="100"
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287 label="Minimum completeness" help="Genomes with lower completeness percentage will be ignored" />
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288 <param argument="--max-contamination" type="float" optional="true" min="0" max="100"
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289 label="Maximum contamination" help="Genomes with higher contamination percentage will be ignored" />
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290 </section>
3
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291 <section name="out" title="Outputs" expanded="false">
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292 <expand macro="output_format"/>
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293 <param argument="--no-zeros" type="boolean" truevalue="--no-zeros" falsevalue="" label="Omit printing of genomes that have zero coverage?" />
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294 <param argument="--dereplication-output-cluster-definition" type="boolean" truevalue="--dereplication-output-cluster-definition" falsevalue="" label="Output a tabular files with dereplicated representatives and member lines?" />
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295 <param argument="--dereplication-output-representative-fasta-directory-copy" type="boolean" truevalue="--dereplication-output-representative-fasta-directory-copy" falsevalue="" label="Output dereplicated representative genomes?" />
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296 </section>
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297 </inputs>
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298 <outputs>
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299 <data name="output" format="tabular" label="${tool.name} on ${on_string}"/>
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300 <data name="cluster_definition" format="tabular" label="${tool.name} on ${on_string}: Cluster definition">
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301 <filter>derep['dereplicate']['dereplicate'] and out['dereplication_output_cluster_definition']</filter>
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302 </data>
3
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303 <collection name="representative_fasta" type="list" label="${tool.name} on ${on_string}: Dereplicated epresentative genomes">
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304 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.fna" format="fasta" directory="representative-fasta" />
3
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305 <filter>derep['dereplicate']['dereplicate'] and out['dereplication_output_representative_fasta_directory_copy']</filter>
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306 </collection>
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307 </outputs>
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308 <tests>
1
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309 <test expect_num_outputs="1">
3
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310 <conditional name="mapped">
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311 <param name="mapped" value="not-mapped" />
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312 <conditional name="mode">
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313 <param name="mode" value="co"/>
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314 <conditional name="read_type">
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315 <param name="type" value="paired_collection"/>
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316 <param name="paired_reads">
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317 <collection type="list:paired">
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318 <element name="reads_for_seq1_and_seq2">
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319 <collection type="paired">
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320 <element name="forward" value="reads_for_seq1_and_seq2.1.fq.gz" ftype="fastqsanger.gz"/>
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321 <element name="reverse" value="reads_for_seq1_and_seq2.2.fq.gz" ftype="fastqsanger.gz"/>
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322 </collection>
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323 </element>
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324 </collection>
3
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325 </param>
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326 </conditional>
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327 <repeat name="extra_reads">
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328 <conditional name="read_type">
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329 <param name="type" value="single"/>
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330 <param name="single" value="reads_for_seq1_and_seq2.fna"/>
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331 </conditional>
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332 </repeat>
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333 <conditional name="genome">
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334 <param name="ref_or_genome" value="contigs"/>
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335 <param name="reference" value="7seqs.fna" />
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336 <conditional name="cond_single_genome">
3
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337 <param name="single_genome" value=""/>
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338 <conditional name="genome_contig_definition">
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339 <param name="choice" value="separator"/>
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340 <param name="separator" value="~"/>
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341 </conditional>
0
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342 </conditional>
3
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343 </conditional>
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344 <param name="sharded" value="" />
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345 </conditional>
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346 </conditional>
3
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347 <param name="exclude_genomes_from_deshard" value="false"/>
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348 <section name="alignment">
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349 <param name="min_read_aligned_length" value="0" />
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350 <param name="min_read_percent_identity" value="0" />
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351 <param name="min_read_aligned_percent" value="0" />
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352 <conditional name="proper_pairs_only">
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353 <param name="proper_pairs_only" value=""/>
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354 </conditional>
3
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355 <param name="exclude_supplementary" value=""/>
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356 </section>
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357 <section name="cov">
3
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358 <param name="methods" value="mean,relative_abundance,variance"/>
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359 <param name="trim_min" value="5"/>
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360 <param name="trim_max" value="95"/>
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361 <param name="min_covered_fraction" value="10"/>
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362 <param name="contig_end_exclusion" value="75"/>
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363 </section>
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364 <section name="derep">
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365 <conditional name="dereplicate">
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366 <param name="dereplicate" value=""/>
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367 </conditional>
0
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368 </section>
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369 <section name="out">
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370 <param name="output_format" value="sparse"/>
3
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371 <param name="no_zeros" value=""/>
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372 <param name="dereplication_output_cluster_definition" value="" />
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373 <param name="dereplication_output_representative_fasta_directory_copy" value="" />
0
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374 </section>
3
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375 <output name="output" ftype="tabular">
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376 <assert_contents>
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377 <has_text text="Sample"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
378 <has_text text="Genome"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
379 <has_text text="Relative Abundance (%)"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
380 <has_text text="Mean"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
381 <has_text text="Variance"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
382 <has_text text="7seqs.fna_0/reads_for_seq1_and_seq2_paired_collection_0"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
383 <has_text text="unmapped"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
384 <has_text text="genome6"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
385 </assert_contents>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
386 </output>
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
387 </test>
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
388 <test expect_num_outputs="1">
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
389 <conditional name="mapped">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
390 <param name="mapped" value="mapped" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
391 <conditional name="mode">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
392 <param name="mode" value="co"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
393 <param name="bam_files" value="7seqs.reads_for_seq1_and_seq2.bam"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
394 <param name="sharded" value="" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
395 <conditional name="genome">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
396 <param name="ref_or_genome" value="contigs"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
397 <conditional name="cond_single_genome">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
398 <param name="single_genome" value=""/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
399 <conditional name="genome_contig_definition">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
400 <param name="choice" value="separator"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
401 <param name="separator" value="~"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
402 </conditional>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
403 </conditional>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
404 </conditional>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
405 <param name="sharded" value="" />
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
406 </conditional>
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
407 </conditional>
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
408 <param name="exclude_genomes_from_deshard" value="false"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
409 <section name="alignment">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
410 <param name="min_read_aligned_length" value="0" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
411 <param name="min_read_percent_identity" value="0" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
412 <param name="min_read_aligned_percent" value="0" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
413 <conditional name="proper_pairs_only">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
414 <param name="proper_pairs_only" value=""/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
415 </conditional>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
416 <param name="exclude_supplementary" value=""/>
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
417 </section>
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
418 <section name="cov">
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
419 <param name="methods" value="mean,relative_abundance"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
420 <param name="trim_min" value="5"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
421 <param name="trim_max" value="95"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
422 <param name="min_covered_fraction" value="10"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
423 <param name="contig_end_exclusion" value="75"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
424 </section>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
425 <section name="derep">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
426 <conditional name="dereplicate">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
427 <param name="dereplicate" value=""/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
428 </conditional>
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
429 </section>
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
430 <section name="out">
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
431 <param name="output_format" value="sparse"/>
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
432 <param name="no_zeros" value=""/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
433 <param name="dereplication_output_cluster_definition" value="" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
434 <param name="dereplication_output_representative_fasta_directory_copy" value="" />
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
435 </section>
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
436 <output name="output" ftype="tabular">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
437 <assert_contents>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
438 <has_text text="Sample"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
439 <has_text text="Genome"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
440 <has_text text="Mean"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
441 <has_text text="7seqs.reads_for_seq1_and_seq2"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
442 <has_text text="genome1"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
443 </assert_contents>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
444 </output>
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
445 </test>
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
446 <test expect_num_outputs="1">
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
447 <conditional name="mapped">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
448 <param name="mapped" value="not-mapped" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
449 <conditional name="mode">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
450 <param name="mode" value="co"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
451 <conditional name="read_type">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
452 <param name="type" value="single"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
453 <param name="single" value="1read.actually_fasta.fq"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
454 </conditional>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
455 <conditional name="genome">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
456 <param name="ref_or_genome" value="genomic"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
457 <conditional name="genomic">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
458 <param name="source" value="history"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
459 <param name="genome_fasta_files" value="500kb.fna,1mbp.fna"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
460 </conditional>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
461 </conditional>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
462 <param name="sharded" value="" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
463 </conditional>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
464 </conditional>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
465 <param name="exclude_genomes_from_deshard" value="false"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
466 <section name="alignment">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
467 <param name="min_read_aligned_length" value="0" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
468 <param name="min_read_percent_identity" value="0" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
469 <param name="min_read_aligned_percent" value="0" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
470 <conditional name="proper_pairs_only">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
471 <param name="proper_pairs_only" value=""/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
472 </conditional>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
473 <param name="exclude_supplementary" value=""/>
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
474 </section>
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
475 <section name="cov">
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
476 <param name="methods" value="covered_bases"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
477 <param name="trim_min" value="5"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
478 <param name="trim_max" value="95"/>
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
479 <param name="min_covered_fraction" value="0"/>
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
480 <param name="contig_end_exclusion" value="75"/>
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
481 </section>
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
482 <section name="derep">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
483 <conditional name="dereplicate">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
484 <param name="dereplicate" value="--dereplicate"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
485 <param name="dereplication_ani" value="99" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
486 <param name="dereplication_aligned_fraction" value="50" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
487 <param name="dereplication_fragment_length" value="3000" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
488 <param name="dereplication_quality_formula" value="Parks2020_reduced" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
489 <param name="dereplication_prethreshold_ani" value="95" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
490 <param name="dereplication_precluster_method" value="finch"/>
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
491 </conditional>
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
492 <param name="genome_info" value="genomeInfo.csv"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
493 </section>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
494 <section name="out">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
495 <param name="output_format" value="sparse"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
496 <param name="no_zeros" value=""/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
497 <param name="dereplication_output_cluster_definition" value="" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
498 <param name="dereplication_output_representative_fasta_directory_copy" value="" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
499 </section>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
500 <output name="output" ftype="tabular">
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
501 <assert_contents>
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
502 <has_text text="Sample"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
503 <has_text text="Genome"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
504 <has_text text="Covered Bases"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
505 <has_text text="1read.actually_fasta.fq_single_0"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
506 <has_text text="1mbp"/>
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
507 </assert_contents>
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
508 </output>
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
509 </test>
1
b6a241c73012 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2388df7187533fb66b7729730340d2eb7b93c112
iuc
parents: 0
diff changeset
510 <test expect_num_outputs="3">
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
511 <conditional name="mapped">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
512 <param name="mapped" value="not-mapped" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
513 <conditional name="mode">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
514 <param name="mode" value="co"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
515 <conditional name="read_type">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
516 <param name="type" value="paired_collection"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
517 <param name="paired_reads">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
518 <collection type="list:paired">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
519 <element name="reads_for_genome2">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
520 <collection type="paired">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
521 <element name="forward" value="reads_for_genome2.1.fa" ftype="fasta"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
522 <element name="reverse" value="reads_for_genome2.2.fa" ftype="fasta"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
523 </collection>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
524 </element>
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
525 </collection>
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
526 </param>
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
527 </conditional>
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
528 <conditional name="genome">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
529 <param name="ref_or_genome" value="genomic"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
530 <conditional name="genomic">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
531 <param name="source" value="history"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
532 <param name="genome_fasta_files" value="genome1.fna,genome2.fna,genome3.fna"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
533 </conditional>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
534 </conditional>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
535 <param name="sharded" value="" />
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
536 </conditional>
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
537 </conditional>
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
538 <param name="exclude_genomes_from_deshard" value="false"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
539 <section name="alignment">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
540 <param name="min_read_aligned_length" value="0" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
541 <param name="min_read_percent_identity" value="0" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
542 <param name="min_read_aligned_percent" value="0" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
543 <conditional name="proper_pairs_only">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
544 <param name="proper_pairs_only" value=""/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
545 </conditional>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
546 <param name="exclude_supplementary" value=""/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
547 </section>
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
548 <section name="cov">
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
549 <param name="methods" value="mean"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
550 <param name="trim_min" value="5"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
551 <param name="trim_max" value="95"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
552 <param name="min_covered_fraction" value="0"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
553 <param name="contig_end_exclusion" value="75"/>
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
554 </section>
1
b6a241c73012 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2388df7187533fb66b7729730340d2eb7b93c112
iuc
parents: 0
diff changeset
555 <section name="derep">
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
556 <conditional name="dereplicate">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
557 <param name="dereplicate" value="--dereplicate"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
558 <param name="dereplication_ani" value="99" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
559 <param name="dereplication_aligned_fraction" value="50" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
560 <param name="dereplication_fragment_length" value="3000" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
561 <param name="dereplication_quality_formula" value="Parks2020_reduced" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
562 <param name="dereplication_prethreshold_ani" value="95" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
563 <param name="dereplication_precluster_method" value="finch"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
564 </conditional>
1
b6a241c73012 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2388df7187533fb66b7729730340d2eb7b93c112
iuc
parents: 0
diff changeset
565 </section>
b6a241c73012 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2388df7187533fb66b7729730340d2eb7b93c112
iuc
parents: 0
diff changeset
566 <section name="out">
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
567 <param name="output_format" value="sparse"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
568 <param name="no_zeros" value=""/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
569 <param name="dereplication_output_cluster_definition" value="true" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
570 <param name="dereplication_output_representative_fasta_directory_copy" value="true" />
1
b6a241c73012 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2388df7187533fb66b7729730340d2eb7b93c112
iuc
parents: 0
diff changeset
571 </section>
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
572 <output name="output" ftype="tabular">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
573 <assert_contents>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
574 <has_text text="Genome"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
575 <has_text text="Mean"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
576 <has_text text="Sample"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
577 <has_text text="reads_for_genome2_paired_collection_0"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
578 <has_text text="genome2"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
579 <has_text text="genome3"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
580 </assert_contents>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
581 </output>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
582 <output name="cluster_definition" ftype="tabular">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
583 <assert_contents>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
584 <has_text text="genome1"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
585 <has_text text="genome2"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
586 <has_text text="genome3"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
587 </assert_contents>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
588 </output>
1
b6a241c73012 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2388df7187533fb66b7729730340d2eb7b93c112
iuc
parents: 0
diff changeset
589 <output_collection name="representative_fasta" type="list" count="3">
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
590 <element name="genome1" ftype="fasta">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
591 <assert_contents>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
592 <has_text text=">random_sequence_length_500_1"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
593 <has_text text=">random_sequence_length_500_2"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
594 </assert_contents>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
595 </element>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
596 <element name="genome2" ftype="fasta">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
597 <assert_contents>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
598 <has_text text=">random_sequence_length_500_1"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
599 <has_text text=">random_sequence_length_500_2"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
600 </assert_contents>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
601 </element>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
602 <element name="genome3" ftype="fasta">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
603 <assert_contents>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
604 <has_text text=">random_sequence_length_500_1"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
605 <has_text text=">random_sequence_length_500_2"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
606 </assert_contents>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
607 </element>
1
b6a241c73012 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2388df7187533fb66b7729730340d2eb7b93c112
iuc
parents: 0
diff changeset
608 </output_collection>
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
609 </test>
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
610 <test expect_num_outputs="1">
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
611 <conditional name="mapped">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
612 <param name="mapped" value="mapped" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
613 <conditional name="mode">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
614 <param name="mode" value="co"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
615 <param name="bam_files" value="2seqs.bad_read.1.with_supplementary.bam"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
616 <param name="sharded" value="" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
617 <conditional name="genome">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
618 <param name="ref_or_genome" value="contigs"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
619 <conditional name="cond_single_genome">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
620 <param name="single_genome" value="true"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
621 <conditional name="genome_contig_definition">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
622 <param name="choice" value="default"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
623 </conditional>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
624 </conditional>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
625 </conditional>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
626 <param name="sharded" value="" />
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
627 </conditional>
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
628 </conditional>
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
629 <param name="exclude_genomes_from_deshard" value="false"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
630 <section name="alignment">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
631 <param name="min_read_aligned_length" value="0" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
632 <param name="min_read_percent_identity" value="0" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
633 <param name="min_read_aligned_percent" value="0" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
634 <conditional name="proper_pairs_only">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
635 <param name="proper_pairs_only" value=""/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
636 </conditional>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
637 <param name="exclude_supplementary" value=""/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
638 </section>
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
639 <section name="cov">
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
640 <param name="methods" value="count"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
641 <param name="trim_min" value="5"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
642 <param name="trim_max" value="95"/>
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
643 <param name="min_covered_fraction" value="0"/>
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
644 <param name="contig_end_exclusion" value="75"/>
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
645 </section>
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
646 <section name="derep" >
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
647 <conditional name="dereplicate">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
648 <param name="dereplicate" value=""/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
649 </conditional>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
650 </section>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
651 <section name="out">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
652 <param name="output_format" value="sparse"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
653 <param name="no_zeros" value=""/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
654 <param name="dereplication_output_cluster_definition" value="" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
655 <param name="dereplication_output_representative_fasta_directory_copy" value="" />
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
656 </section>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
657 <output name="output" ftype="tabular">
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
658 <assert_contents>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
659 <has_text text="Sample"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
660 <has_text text="Genome"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
661 <has_text text="Read Count"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
662 <has_text text="2seqs.bad_read.1.with_supplementary"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
663 <has_text text="genome1"/>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
664 </assert_contents>
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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665 </output>
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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666 </test>
3
dd96e74908a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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667 </tests>
0
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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668 <help><![CDATA[
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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669 .. class:: infomark
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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670
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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671 **Dereplication quality formula**
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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672
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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673 Scoring function for genome quality:
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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674
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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675 - Parks2020_reduced: A quality formula described in `Parks et. al. 2020 <https://doi.org/10.1038/s41587-020-0501-8>`_ (Supplementary Table 19) but only including those scoring criteria that can be calculated from the sequence without homology searching: *completeness-5*contamination-5*num_contigs/100-5*num_ambiguous_bases/100000*.
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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676 - completeness-4contamination: *completeness-4*contamination*
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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677 - completeness-5contamination: *completeness-5*contamination*
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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678 - dRep: *completeness-5*contamination+contamination*(strain_heterogeneity/100)+0.5*log10(N50)*
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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679
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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680 -----
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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681
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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682 .. class:: infomark
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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683
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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684 **Method for calculating coverage**
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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685
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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686 Calculation of genome-wise coverage (genome mode) is similar to calculating contig-wise (contig mode) coverage, except that the unit of reporting is per-genome rather than per-contig. For calculation methods which exclude base positions based on their coverage, all positions from all contigs are considered together.
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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687
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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688 - Relative abundance: Percentage relative abundance of each genome, and the unmapped read percentage
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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689 - Mean: Average number of aligned reads overlapping each position on the genome
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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690 - Trimmed mean: Average number of aligned reads overlapping each position after removing the most deeply and shallowly covered positions.
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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691 - Covered fraction: Fraction of genome covered by 1 or more reads
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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692 - Covered bases: Number of bases covered by 1 or more reads
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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693 - Variance: Variance of coverage depths
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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694 - Length: Length of each genome in base pairs
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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695 - Count: Number of reads aligned toq each genome. Note that a single read may be aligned to multiple genomes with supplementary alignments
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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696 - Reads per base: Number of reads aligned divided by the length of the genome
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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697 - MetaBAT: Reproduction of the `MetaBAT <https://bitbucket.org/berkeleylab/metabat>`_ tool output
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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698 - Coverage histogram: Histogram of coverage depths
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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699 - RPKM: Reads mapped per kilobase of genome, per million mapped reads
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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700 - TPM: Transcripts Per Million as described in `Li et al 2010 <https://doi.org/10.1093/bioinformatics/btp692>`_
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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701
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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702 ]]></help>
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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703 <expand macro="citation"/>
5901cc218127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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704 </tool>