Mercurial > repos > iuc > coverm_contig

annotate coverm_contig.xml @ 6:28d740f2c0b0 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit f5876e043d748c5bdb6d310396dd2b34f30ae23a
author iuc
date Sun, 25 Feb 2024 09:45:07 +0000
parents 1dcea261abbe
children
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688a777e1b19 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2388df7187533fb66b7729730340d2eb7b93c112
iuc
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1 <tool id="coverm_contig" name="CoverM contig" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Calculate read coverage per contig</description>
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3 <macros>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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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"/>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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8 <command><![CDATA[
3
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9 #import re
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10 #import os
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11
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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12 #set $single_fp = []
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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13 #set $fw_fp = []
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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14 #set $rv_fp = []
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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15 #set $interl_fp = []
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16 #set $ref_fp = []
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17 #set $bam_fp = []
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18
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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19 mkdir 'single/' &&
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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20 mkdir 'fw/' &&
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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21 mkdir 'rv/' &&
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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22 mkdir 'interl/' &&
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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23 mkdir 'ref/' &&
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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24 mkdir 'bam/' &&
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25
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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26 #if $mapped.mapped == 'mapped'
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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27 @BAMS@
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28 #else
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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29 #if $mapped.mode.mode == 'individual'
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30 @INDIVIDUAL_ASSEMBLY_READS@
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31 #set $ref = $mapped.mode.reference
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32 @INDIVIDUAL_ASSEMBLY_REF@
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33 #else
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34 @CO_ASSEMBLY_ALL_READS@
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35 #set $refs = $mapped.mode.reference
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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36 @CO_ASSEMBLY_REF@
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37 #end if
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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38 #end if
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39
3
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40 coverm
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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41 contig
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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42 #if $mapped.mapped == 'mapped'
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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43 -b
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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44 #for $bam in $bam_fp
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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45 '$bam'
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46 #end for
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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47 $mapped.sharded
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48 #else
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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49 #if $fw_fp
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50 -1
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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51 #for $read in $fw_fp
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52 '$read'
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53 #end for
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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54 -2
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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55 #for $read in $rv_fp
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56 '$read'
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57 #end for
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58 #else if $single_fp
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59 --single
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60 #for $read in $single_fp
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61 '$read'
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62 #end for
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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63 #else if $interl_fp
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64 --interleaved
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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65 #for $read in $interl_fp
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66 '$read'
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67 #end for
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68 #end if
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69 --reference
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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70 #for $ref in $ref_fp
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71 '$ref'
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72 #end for
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73 #if $mapped.mode.mode == 'co'
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74 $mapped.mode.sharded
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75 #end if
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76 --mapper '$mapped.mapper'
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77 #end if
0
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78
3
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79 --min-read-aligned-length $alignment.min_read_aligned_length
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80 --min-read-percent-identity $alignment.min_read_percent_identity
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81 --min-read-aligned-percent $alignment.min_read_aligned_percent
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82 $alignment.proper_pairs_only.proper_pairs_only
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83 #if $alignment.proper_pairs_only.proper_pairs_only != ''
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84 --min-read-aligned-length-pair $alignment.proper_pairs_only.min_read_aligned_length_pair
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85 --min-read-percent-identity-pair $alignment.proper_pairs_only.min_read_percent_identity_pair
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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86 --min-read-aligned-percent-pair $alignment.proper_pairs_only.min_read_aligned_percent_pair
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87 #end if
0
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88
3
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89 --methods
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90 #for method in $cov.methods
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91 '$method'
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92 #end for
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93 --min-covered-fraction $cov.min_covered_fraction
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94 --contig-end-exclusion $cov.contig_end_exclusion
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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95 --trim-min $cov.trim_min
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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96 --trim-max $cov.trim_max
0
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97
3
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98 --output-format '$output_format'
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99 --output-file '$output'
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100 --threads \${GALAXY_SLOTS:-1}
0
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101 ]]></command>
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102 <inputs>
3
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103 <conditional name="mapped">
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104 <expand macro="mapped"/>
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105 <when value="mapped">
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106 <expand macro="mapped_params"/>
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107 </when>
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108 <when value="not-mapped">
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109 <conditional name="mode">
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110 <expand macro="assembly_mode"/>
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111 <when value="individual">
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112 <expand macro="individual_assembly_reads"/>
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113 <expand macro="individual_assembly_reference"/>
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114 </when>
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115 <when value="co">
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116 <expand macro="co_assembly_reads"/>
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117 <repeat name="extra_reads" title="Additional reads">
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118 <expand macro="co_assembly_reads"/>
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119 </repeat>
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120 <expand macro="co_assembly_reference"/>
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121 </when>
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122 </conditional>
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123 <expand macro="mapping"/>
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124 </when>
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125 </conditional>
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126 <expand macro="alignment"/>
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127 <section name="cov" title="Coverage calculation options" expanded="false">
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128 <param argument="--methods" type="select" multiple="true" label="Method(s) for calculating coverage">
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129 <option value="mean" selected="true">mean: Average number of aligned reads overlapping each position on the contig</option>
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130 <expand macro="cov_method_options"/>
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131 </param>
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132 <expand macro="coverage_params"/>
0
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133 </section>
3
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134 <expand macro="output_format"/>
0
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135 </inputs>
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136 <outputs>
3
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137 <data name="output" format="tabular"/>
0
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138 </outputs>
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139 <tests>
3
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140 <test expect_num_outputs="1">
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141 <conditional name="mapped">
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142 <param name="mapped" value="not-mapped" />
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143 <conditional name="mode">
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144 <param name="mode" value="co"/>
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145 <conditional name="read_type">
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146 <param name="type" value="paired_collection"/>
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147 <param name="paired_reads">
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148 <collection type="list:paired">
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149 <element name="reads_for_seq1_and_seq2">
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150 <collection type="paired">
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151 <element name="forward" value="reads_for_seq1_and_seq2.1.fq.gz" ftype="fastqsanger.gz"/>
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152 <element name="reverse" value="reads_for_seq1_and_seq2.2.fq.gz" ftype="fastqsanger.gz"/>
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153 </collection>
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154 </element>
0
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155 </collection>
3
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156 </param>
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157 </conditional>
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158 <param name="reference" value="7seqs.fna" />
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159 <param name="sharded" value="" />
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160 </conditional>
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161 </conditional>
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162 <section name="alignment">
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163 <param name="min_read_aligned_length" value="0" />
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164 <param name="min_read_percent_identity" value="0" />
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165 <param name="min_read_aligned_percent" value="0" />
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166 <conditional name="proper_pairs_only">
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167 <param name="proper_pairs_only" value=""/>
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168 </conditional>
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169 <param name="exclude_supplementary" value=""/>
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170 </section>
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171 <section name="cov">
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172 <param name="methods" value="mean"/>
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173 <param name="trim_min" value="5"/>
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174 <param name="trim_max" value="95"/>
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175 <param name="min_covered_fraction" value="10"/>
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176 <param name="contig_end_exclusion" value="75"/>
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177 </section>
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178 <param name="output_format" value="dense"/>
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179 <output name="output" ftype="tabular">
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180 <assert_contents>
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181 <has_text text="Contig"/>
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182 <has_text text="Mean"/>
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183 <has_text text="7seqs.fna"/>
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184 <has_text text="genome1~random_sequence_length_11000"/>
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185 <has_text text="genome2~seq1"/>
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186 </assert_contents>
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187 </output>
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188 </test>
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189 <test expect_num_outputs="1">
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190 <conditional name="mapped">
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191 <param name="mapped" value="not-mapped" />
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192 <conditional name="mode">
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193 <param name="mode" value="individual"/>
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194 <conditional name="read_type">
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195 <param name="type" value="paired"/>
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196 <param name="read1" value="reads_for_seq1_and_seq2.1.fq.gz" ftype="fastqsanger.gz"/>
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197 <param name="read2" value="reads_for_seq1_and_seq2.2.fq.gz" ftype="fastqsanger.gz"/>
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198 </conditional>
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199 <param name="reference" value="7seqs.fna" />
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200 <param name="sharded" value="" />
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201 </conditional>
0
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202 </conditional>
3
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203 <section name="alignment">
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204 <param name="min_read_aligned_length" value="0" />
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205 <param name="min_read_percent_identity" value="0" />
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206 <param name="min_read_aligned_percent" value="0" />
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207 <conditional name="proper_pairs_only">
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208 <param name="proper_pairs_only" value=""/>
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209 </conditional>
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210 <param name="exclude_supplementary" value=""/>
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211 </section>
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212 <section name="cov">
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213 <param name="methods" value="mean"/>
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214 <param name="trim_min" value="5"/>
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215 <param name="trim_max" value="95"/>
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216 <param name="min_covered_fraction" value="10"/>
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217 <param name="contig_end_exclusion" value="75"/>
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218 </section>
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219 <param name="output_format" value="dense"/>
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220 <output name="output" ftype="tabular">
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221 <assert_contents>
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222 <has_text text="Contig"/>
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223 <has_text text="Mean"/>
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224 <has_text text="7seqs.fna"/>
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225 <has_text text="genome1~random_sequence_length_11000"/>
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226 <has_text text="genome2~seq1"/>
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227 </assert_contents>
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228 </output>
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229 </test>
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230 <test expect_num_outputs="1">
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231 <conditional name="mapped">
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232 <param name="mapped" value="not-mapped" />
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233 <conditional name="mode">
4
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234 <param name="mode" value="individual"/>
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235 <conditional name="read_type">
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236 <param name="type" value="paired_collection"/>
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237 <param name="paired_reads">
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238 <collection type="paired">
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239 <element name="forward" value="reads_for_seq1_and_seq2.1.fq.gz" ftype="fastqsanger.gz"/>
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240 <element name="reverse" value="reads_for_seq1_and_seq2.2.fq.gz" ftype="fastqsanger.gz"/>
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241 </collection>
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242 </param>
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243 </conditional>
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244 <param name="reference" value="7seqs.fna" />
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245 <param name="sharded" value="" />
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246 </conditional>
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247 </conditional>
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248 <section name="alignment">
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249 <param name="min_read_aligned_length" value="0" />
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250 <param name="min_read_percent_identity" value="0" />
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251 <param name="min_read_aligned_percent" value="0" />
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252 <conditional name="proper_pairs_only">
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253 <param name="proper_pairs_only" value=""/>
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254 </conditional>
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255 <param name="exclude_supplementary" value=""/>
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256 </section>
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257 <section name="cov">
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258 <param name="methods" value="mean"/>
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259 <param name="trim_min" value="5"/>
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260 <param name="trim_max" value="95"/>
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261 <param name="min_covered_fraction" value="10"/>
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262 <param name="contig_end_exclusion" value="75"/>
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263 </section>
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264 <param name="output_format" value="dense"/>
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265 <output name="output" ftype="tabular">
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266 <assert_contents>
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267 <has_text text="Contig"/>
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268 <has_text text="Mean"/>
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269 <has_text text="7seqs.fna"/>
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270 <has_text text="genome1~random_sequence_length_11000"/>
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271 <has_text text="genome2~seq1"/>
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272 </assert_contents>
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273 </output>
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274 </test>
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275 <test expect_num_outputs="1">
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276 <conditional name="mapped">
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277 <param name="mapped" value="not-mapped" />
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278 <conditional name="mode">
3
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279 <param name="mode" value="co"/>
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280 <conditional name="read_type">
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281 <param name="type" value="single"/>
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282 <param name="single" value="bad_reads.interleaved.fq"/>
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283 </conditional>
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284 <param name="reference" value="2seqs.fasta" />
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285 <param name="sharded" value="" />
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286 </conditional>
0
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287 </conditional>
3
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parents: 2
diff changeset
288 <section name="alignment">
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iuc
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289 <param name="min_read_aligned_length" value="0" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
290 <param name="min_read_percent_identity" value="0" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
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291 <param name="min_read_aligned_percent" value="0" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
292 <conditional name="proper_pairs_only">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
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293 <param name="proper_pairs_only" value=""/>
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294 </conditional>
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iuc
parents: 2
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295 <param name="exclude_supplementary" value=""/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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296 </section>
0
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iuc
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297 <section name="cov">
3
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298 <param name="methods" value="mean"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
299 <param name="trim_min" value="5"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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300 <param name="trim_max" value="95"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
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301 <param name="min_covered_fraction" value="10"/>
0
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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302 <param name="contig_end_exclusion" value="0"/>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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303 </section>
3
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304 <param name="output_format" value="sparse"/>
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iuc
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305 <output name="output" ftype="tabular">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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306 <assert_contents>
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iuc
parents: 2
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307 <has_text text="Contig"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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308 <has_text text="Mean"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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309 <has_text text="Sample"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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310 <has_text text="2seqs.fasta_0/bad_reads.interleaved.fq_single_0"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
311 <has_text text="seq2"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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312 </assert_contents>
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iuc
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313 </output>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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314 </test>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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diff changeset
315 <test expect_num_outputs="1">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
316 <conditional name="mapped">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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317 <param name="mapped" value="not-mapped" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
318 <conditional name="mode">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
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319 <param name="mode" value="co"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
320 <conditional name="read_type">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
321 <param name="type" value="interleaved"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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diff changeset
322 <param name="interleaved" value="bad_reads.all.interleaved.fa"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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323 </conditional>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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diff changeset
324 <param name="reference" value="2seqs.fasta" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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diff changeset
325 <param name="sharded" value="" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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diff changeset
326 </conditional>
0
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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327 </conditional>
3
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
328 <section name="alignment">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
329 <param name="min_read_aligned_length" value="0" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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diff changeset
330 <param name="min_read_percent_identity" value="0" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
331 <param name="min_read_aligned_percent" value="0" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
332 <conditional name="proper_pairs_only">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
333 <param name="proper_pairs_only" value=""/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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diff changeset
334 </conditional>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
335 <param name="exclude_supplementary" value=""/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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diff changeset
336 </section>
0
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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337 <section name="cov">
3
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
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parents: 2
diff changeset
338 <param name="methods" value="mean"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
339 <param name="trim_min" value="5"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
340 <param name="trim_max" value="95"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
341 <param name="min_covered_fraction" value="10"/>
0
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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342 <param name="contig_end_exclusion" value="0"/>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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343 </section>
3
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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diff changeset
344 <param name="output_format" value="sparse"/>
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iuc
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345 <output name="output" ftype="tabular">
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iuc
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346 <assert_contents>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
347 <has_text text="Contig"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
348 <has_text text="Mean"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
349 <has_text text="Sample"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
350 <has_text text="2seqs.fasta_0/bad_reads.all.interleaved.fa_interleaved_0"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
351 <has_text text="seq1"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
352 <has_text text="seq2"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
353 </assert_contents>
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iuc
parents: 2
diff changeset
354 </output>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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355 </test>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
356 <test expect_num_outputs="1">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
357 <conditional name="mapped">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
358 <param name="mapped" value="not-mapped" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
359 <conditional name="mode">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
360 <param name="mode" value="co"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
361 <conditional name="read_type">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
362 <param name="type" value="paired"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
363 <param name="read1" value="reads_for_seq1_and_seq2.1.fq.gz"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
364 <param name="read2" value="reads_for_seq1_and_seq2.2.fq.gz"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
365 </conditional>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
366 <repeat name="extra_reads">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
367 <conditional name="read_type">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
368 <param name="type" value="paired_collection"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
369 <param name="paired_reads">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
370 <collection type="list:paired">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
371 <element name="reads_for_seq1_and_seq2">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
372 <collection type="paired">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
373 <element name="forward" value="reads_for_seq1_and_seq2.1.fq.gz" ftype="fastqsanger.gz"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
374 <element name="reverse" value="reads_for_seq1_and_seq2.2.fq.gz" ftype="fastqsanger.gz"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
375 </collection>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
376 </element>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
377 </collection>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
378 </param>
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iuc
parents: 2
diff changeset
379 </conditional>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
380 </repeat>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
381 <param name="reference" value="2seqs.fasta" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
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diff changeset
382 <param name="sharded" value="" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
383 </conditional>
0
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
384 </conditional>
3
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
385 <section name="alignment">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
386 <param name="min_read_aligned_length" value="0" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
387 <param name="min_read_percent_identity" value="0.95" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
388 <param name="min_read_aligned_percent" value="0" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
389 <conditional name="proper_pairs_only">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
390 <param name="proper_pairs-only" value=""/>
0
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
391 </conditional>
3
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
392 <param name="exclude_supplementary" value=""/>
0
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
393 </section>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
394 <section name="cov">
3
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
395 <param name="methods" value="mean"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
396 <param name="trim_min" value="5"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
397 <param name="trim_max" value="95"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
398 <param name="min_covered_fraction" value="10"/>
0
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
399 <param name="contig_end_exclusion" value="0"/>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
400 </section>
3
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
401 <param name="output_format" value="sparse"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
402 <output name="output" ftype="tabular">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
403 <assert_contents>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
404 <has_text text="Contig"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
405 <has_text text="Mean"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
406 <has_text text="Sample"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
407 <has_text text="2seqs.fasta_0/reads_for_seq1_and_seq2.1.fq.gz_paired_0"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
408 <has_text text="2seqs.fasta_0/reads_for_seq1_and_seq2_paired_collection_00"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
409 <has_text text="seq1"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
410 <has_text text="seq2"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
411 </assert_contents>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
412 </output>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
413 </test>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
414 <test expect_num_outputs="1">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
415 <conditional name="mapped">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
416 <param name="mapped" value="mapped" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
417 <conditional name="mode">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
418 <param name="mode" value="co"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
419 <param name="bam_files" value="tpm_test.bam"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
420 <param name="sharded" value="" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
421 </conditional>
0
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
422 </conditional>
3
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
423 <section name="alignment">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
424 <param name="min_read_aligned_length" value="0" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
425 <param name="min_read_percent_identity" value="0.95" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
426 <param name="min_read_aligned_percent" value="0" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
427 <conditional name="proper_pairs_only">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
428 <param name="proper_pairs-only" value=""/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
429 </conditional>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
430 <param name="exclude_supplementary" value=""/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
431 </section>
0
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
432 <section name="cov">
3
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
433 <param name="methods" value="mean,tpm"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
434 <param name="trim_min" value="5"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
435 <param name="trim_max" value="95"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
436 <param name="min_covered_fraction" value="10"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
437 <param name="contig_end_exclusion" value="75"/>
0
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
438 </section>
3
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
439 <param name="output_format" value="sparse"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
440 <output name="output" ftype="tabular">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
441 <assert_contents>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
442 <has_text text="Contig"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
443 <has_text text="Mean"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
444 <has_text text="Sample"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
445 <has_text text="TPM"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
446 <has_text text="tpm_test"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
447 <has_text text="genome1~random_sequence_length_11000"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
448 <has_text text="genome2~seq1"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
449 <has_text text="genome3~random_sequence_length_11001"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
450 </assert_contents>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
451 </output>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
452 </test>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
453 <test expect_num_outputs="1">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
454 <conditional name="mapped">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
455 <param name="mapped" value="mapped" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
456 <conditional name="mode">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
457 <param name="mode" value="co"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
458 <param name="bam_files" value="tpm_test.bam"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
459 <param name="sharded" value="" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
460 </conditional>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
461 </conditional>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
462 <section name="alignment">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
463 <param name="min_read_aligned_length" value="0" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
464 <param name="min_read_percent_identity" value="0.95" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
465 <param name="min_read_aligned_percent" value="0" />
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
466 <conditional name="proper_pairs_only">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
467 <param name="proper_pairs-only" value=""/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
468 </conditional>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
469 <param name="exclude_supplementary" value=""/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
470 </section>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
471 <section name="cov">
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
472 <param name="methods" value="mean,tpm"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
473 <param name="trim_min" value="5"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
474 <param name="trim_max" value="95"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
475 <param name="min_covered_fraction" value="10"/>
c2a5823e4763 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
iuc
parents: 2
diff changeset
476 <param name="contig_end_exclusion" value="75"/>
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477 </section>
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478 <param name="output_format" value="sparse"/>
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479 <output name="output" ftype="tabular">
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480 <assert_contents>
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481 <has_text text="Contig"/>
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482 <has_text text="Mean"/>
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483 <has_text text="Sample"/>
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484 <has_text text="TPM"/>
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485 <has_text text="tpm_test"/>
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486 <has_text text="genome1~random_sequence_length_11000"/>
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487 <has_text text="genome2~seq1"/>
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488 <has_text text="genome3~random_sequence_length_11001"/>
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489 </assert_contents>
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490 </output>
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491 </test>
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492 </tests>
0
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493 <help><![CDATA[
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494 .. class:: infomark
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495
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496 **Method for calculating coverage**
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497
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498 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.
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499
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500 - Relative abundance: Percentage relative abundance of each genome, and the unmapped read percentage
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501 - Mean: Average number of aligned reads overlapping each position on the genome
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502 - Trimmed mean: Average number of aligned reads overlapping each position after removing the most deeply and shallowly covered positions.
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503 - Covered fraction: Fraction of genome covered by 1 or more reads
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504 - Covered bases: Number of bases covered by 1 or more reads
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505 - Variance: Variance of coverage depths
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506 - Length: Length of each genome in base pairs
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507 - Count: Number of reads aligned toq each genome. Note that a single read may be aligned to multiple genomes with supplementary alignments
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508 - Reads per base: Number of reads aligned divided by the length of the genome
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509 - MetaBAT: Reproduction of the `MetaBAT <https://bitbucket.org/berkeleylab/metabat>`_ tool output
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510 - Coverage histogram: Histogram of coverage depths
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511 - RPKM: Reads mapped per kilobase of genome, per million mapped reads
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512 - TPM: Transcripts Per Million as described in `Li et al 2010 <https://doi.org/10.1093/bioinformatics/btp692>`_
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513
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514 ]]></help>
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515 <expand macro="citation"/>
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516 </tool>